This document chronicles the analysis from the data as it is exported as median signaling and event counts from nolanlab.cytobank.org.
Load the necessary packages:
library(dplyr)
library(reshape2)
library(tidyr)
library(blackbuck)
library(FDAlibrary)
library(ggplot2)
library(samr)
Load the signaling data:
setwd("~/Documents/neonatal")
dataDirectory <- "./exported_statistics/"
raw_df <- read.csv(paste(dataDirectory, "neonatals-medians.csv", sep = ""))
figure_directory <- "./figure_graphs/"
Clean Cytobank output for our uses.
raw_df <- raw_df %>%
tidyr::separate(col = Conditions, into = c("SampleType", "Conditions"), sep = "_") %>%
dplyr::select(-(FCS.Filename)) %>%
dplyr::rename(Pair = Individuals) %>%
dplyr::mutate(Individual = as.factor(paste(Pair, SampleType, sep = "_"))) %>%
dplyr::rename(Condition = Conditions) %>%
dplyr::select(-contains("Singlets")) %>%
dplyr::select(-contains("Mononuclear"))
annotation_columns = c("Individual", "Pair","SampleType", "Condition")
Now we have the following attributes as columns
Name cleaning:
Generate fold change data (arcsinh ratio) for LPS and cocktail:
fold_df <- get_folds(raw_df, basal_name = "unstim", fold_type = "asinh", unique_IDs = "filename",
annotation_columns = annotation_columns)
LPS_df <- dplyr::filter(fold_df, Condition == "LPS")
Cocktail_df <- dplyr::filter(fold_df, Condition == "Cocktail")
And select and transform the unstim data:
unstim_df <- dplyr::filter(raw_df, Condition == "unstim")
unstim_df <- reshape2::melt(unstim_df)
unstim_df$value <- asinh(unstim_df$value / 5)
unstim_df <- reshape2::dcast(unstim_df, ... ~ variable)
unstim_df <- dplyr::select(unstim_df, -filename)
Unstim_df <- unstim_df
Now we have data frames corresponding to each condition (Unstim_df, LPS_df, and Cocktail_df) to work with in the analysis.
We additionally want to load and clean the abundance data and calculate percent totals.
setwd("~/Documents/neonatal/")
abundance_df <- read.csv(paste(dataDirectory, "neonatals-abundances.csv", sep = ""))
abundance_df <- abundance_df %>%
tidyr::separate(col = Conditions, into = c("SampleType", "Conditions"), sep = "_") %>%
dplyr::select(-(FCS.Filename)) %>%
dplyr::rename(Pair = Individuals) %>%
dplyr::mutate(Individual = as.factor(paste(Pair, SampleType, sep = "_"))) %>%
dplyr::rename(Condition = Conditions) %>%
dplyr::filter(Condition == "unstim")
Calculate percentages:
base_counts <- abundance_df$Mononuclearcells_EventCounts
singlet_counts <- abundance_df$Singlets_EventCounts
cell_types <- abundance_df[,!(names(abundance_df) %in% c(annotation_columns,
"Singlets_EventCounts",
"Mononuclearcells_EventCounts",
"Granulocytes_EventCounts", "filename"))]
grans <- abundance_df$Granulocytes_EventCounts
percents <- cbind(cell_types/base_counts, Granulocytes_EventCounts = grans/singlet_counts)
percents_df <- data.frame(filename = abundance_df$filename, abundance_df[, colnames(abundance_df) %in% annotation_columns], percents)
# write.csv(percents_df, file = "~/Documents/neonatal/neonatals_percentages.csv")
Now the data frame percents_df has the percent totals of all populations as percentage of mononuclear cells, with the exception of granulocytes which are as a percent of singlets.
Name cleaning for abundances:
Generate response varaible y for Two Class Paired (Mom and Baby)
# SAMDirectory <- "~/Documents/neonatal/SAM/"
y <- dplyr::select(unstim_df, Pair, SampleType)
y <- cbind(y, resp = rep(1:10, each = 2))
for (i in 1:nrow(y)){
if ( y[i, "SampleType"] == "B"){
y[i, "resp"] <- -(y[i, "resp"])
}
}
y <- y$resp
Run SAM model
# generated percents_df (includes annotations) and percents (numeric only)
x <- percents
runSAM <- function(){
sink("/dev/null")
model <- SAM(t(x), y, genenames = colnames(x), resp.type = "Two class paired", nperms = 1000, fdr.output = 0.01)
sink()
return(model)
}
model <- runSAM()
sig.up <- model$siggenes.table$genes.up[model$siggenes.table$genes.up[,"q-value(%)"] == "0", ]
# Higher in Mom
print(sig.up)
## Gene ID Gene Name Score(d) Numerator(r)
## [1,] "Memory_CD4_T_cells_Percent_Total" "18" "6.219" "0.096"
## [2,] "CD8_T_cells_Percent_Total" "1" "4.465" "0.078"
## [3,] "Memory_CD8_T_cells_Percent_Total" "5" "4.007" "0.059"
## [4,] "Granulocytes_Percent_Total" "19" "3.361" "0.135"
## [5,] "Th1_T_cells_Percent_Total" "11" "2.757" "0.019"
## [6,] "gd_T_cells_Percent_Total" "17" "2.336" "0.009"
## [7,] "Naive_CD8_T_cells_Percent_Total" "4" "2.115" "0.02"
## Denominator(s+s0) Fold Change q-value(%)
## [1,] "0.015" "2.163" "0"
## [2,] "0.017" "1.555" "0"
## [3,] "0.015" "2.82" "0"
## [4,] "0.04" "1.452" "0"
## [5,] "0.007" "13.376" "0"
## [6,] "0.004" "3.112" "0"
## [7,] "0.009" "1.181" "0"
sig.lo <- model$siggenes.table$genes.lo[model$siggenes.table$genes.lo[,"q-value(%)"] == "0", ]
# Higher in Baby
print(sig.lo)
## Gene ID Gene Name Score(d) Numerator(r)
## [1,] "B_cells_Percent_Total" "6" "-6.613" "-0.104"
## [2,] "Naive_CD4_T_cells_Percent_Total" "3" "-2.929" "-0.094"
## [3,] "CD56lo_NK_cells_Percent_Total" "15" "-1.957" "-0.007"
## [4,] "MDSCs_Percent_Total" "13" "-1.858" "-0.008"
## Denominator(s+s0) Fold Change q-value(%)
## [1,] "0.016" "0.457" "0"
## [2,] "0.032" "0.708" "0"
## [3,] "0.004" "0.669" "0"
## [4,] "0.004" "0.536" "0"
sigs <- rbind(sig.up, sig.lo)
# write.csv(sigs, file = paste(SAMDirectory, "percent_mononuclear_fdr_0.01.csv", sep = ""))
df <- percents_df
sig_df <- data.frame(sigs)
feat_vals <- cbind(Individual = df$Individual, df[, colnames(df) %in% sig_df$Gene.ID])
# write.csv(feat_vals, file = paste(SAMDirectory, "percent_mononuclear_feature_values_fdr_0.01.csv", sep = ""))
df <- melt(df)
## Using filename, SampleType, Condition, Pair, Individual as id variables
df <- df[df[, "variable"] %in% sig_df$Gene.ID,]
ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip()
# log scale
ggplot(df, aes(variable, log10(value))) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip() + scale_color_brewer(palette = "Dark2") + theme_bw()
# #ggsave(filename = paste(figure_directory, "abundances_sig_plot.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)
# #ggsave(filename = paste(figure_directory, "abundances_sig_plot2.pdf", sep = ""), width = 30, height = 20, useDingbats=FALSE)
# plot all
df <- percents_df
df <- reshape2::melt(df)
## Using filename, SampleType, Condition, Pair, Individual as id variables
ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip()
# log scale
ggplot(df, aes(variable, log10(value))) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Abundance differences (% Mononuclear cells)") + coord_flip() + scale_color_brewer(palette = "Dark2") + theme_bw()
# #ggsave(filename = paste(SAMDirectory, "percent_mononuclear_all_plot.pdf", sep = ""), width = 30, height = 20)
Features that are not significant based on the estimated Q-val = 0:
not_sig <- percents_df[,!(colnames(percents_df) %in% sig_df$Gene.ID)]
colnames(dplyr::select(not_sig, contains("EventCounts")))
## character(0)
Might want to include Scaffold in this figure.
Confidence intervals: (1 is significant, i.e. interval does not include zero)
mom_df <- percents_df %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
baby_df <- percents_df %>% dplyr::filter(SampleType == "B") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
conf_int <- mapply(function(x, y) t.test(x,y, paired = TRUE)$conf.int[1:2], mom_df, baby_df)
conf_int <- t(conf_int)
colnames(conf_int) <- c("lower_bound", "upper_bound")
interval_no_zero <- sign(conf_int[, "lower_bound"]) == sign(conf_int[, "upper_bound"])
cbind(conf_int, interval_no_zero)
## lower_bound upper_bound
## CD8_T_cells_Percent_Total 0.0401081357 1.155168e-01
## CD4_T_cells_Percent_Total -0.0807887193 8.351260e-02
## Naive_CD4_T_cells_Percent_Total -0.1644497247 -2.308146e-02
## Naive_CD8_T_cells_Percent_Total 0.0003669442 3.870683e-02
## Memory_CD8_T_cells_Percent_Total 0.0273439822 9.032883e-02
## B_cells_Percent_Total -0.1372103743 -6.983107e-02
## Classical_monocytes_Percent_Total -0.0523618634 4.152444e-02
## Nonclassical_monocytes_Percent_Total -0.0016454460 4.994231e-03
## cDCs_Percent_Total -0.0425593280 5.395465e-02
## pDCs_Percent_Total 0.0004260802 1.508539e-03
## Th1_T_cells_Percent_Total 0.0051520612 3.309257e-02
## Intermediate_monocytes_Percent_Total -0.0019590055 4.552569e-03
## MDSCs_Percent_Total -0.0154941425 -3.119472e-05
## Tregs_Percent_Total -0.0039976574 1.249058e-03
## CD56lo_NK_cells_Percent_Total -0.0130613427 -6.530414e-04
## CD56hi_NK_cells_Percent_Total -0.0004596581 3.247199e-03
## gd_T_cells_Percent_Total 0.0020075346 1.602777e-02
## Memory_CD4_T_cells_Percent_Total 0.0628400793 1.292807e-01
## Granulocytes_Percent_Total 0.0458562559 2.242088e-01
## interval_no_zero
## CD8_T_cells_Percent_Total 1
## CD4_T_cells_Percent_Total 0
## Naive_CD4_T_cells_Percent_Total 1
## Naive_CD8_T_cells_Percent_Total 1
## Memory_CD8_T_cells_Percent_Total 1
## B_cells_Percent_Total 1
## Classical_monocytes_Percent_Total 0
## Nonclassical_monocytes_Percent_Total 0
## cDCs_Percent_Total 0
## pDCs_Percent_Total 1
## Th1_T_cells_Percent_Total 1
## Intermediate_monocytes_Percent_Total 0
## MDSCs_Percent_Total 1
## Tregs_Percent_Total 0
## CD56lo_NK_cells_Percent_Total 1
## CD56hi_NK_cells_Percent_Total 0
## gd_T_cells_Percent_Total 1
## Memory_CD4_T_cells_Percent_Total 1
## Granulocytes_Percent_Total 1
Running PCA on entire signaling dataset:
dfs <- list("LPS" = LPS_df, "Cocktail" = Cocktail_df, "Unstim" = Unstim_df)
df <- do.call(cbind, args = dfs)
df_num <- df %>% dplyr::select(-contains("Individual"), -contains("Pair"), - contains("SampleType"), -contains("Condition"))
x <- as.matrix(df_num)
pr.out <- prcomp(x, scale = FALSE)
transformed_x <- pr.out$x
PC_df <- data.frame(transformed_x, Individual = unstim_df$Individual, SampleType = unstim_df$SampleType, Pair = unstim_df$Pair)
loadings1 <- pr.out$rotation[, "PC1"]
loadings2 <- pr.out$rotation[, "PC2"]
Plotting PCA, coloring by population shows that PC1 separates the Mom and Baby populations:
# plotting
pca <- ggplot(PC_df, aes(PC1, PC2, group = Pair))
pca + geom_point(size = 2, aes(colour = SampleType)) + scale_color_brewer(palette = "Dark2") + theme_bw() + ggtitle("PCA by population")
#ggsave(paste(figure_directory, "PCA_by_population.pdf"), width = 5, height = 4, useDingbats=FALSE)
PC2 separates by pair:
pca + geom_point(size = 2, aes(colour = Pair)) + ggtitle("PCA by mom-baby pair") + geom_line(aes(colour = Pair))
# #ggsave(paste(pairedDirectory, "PCA_by_pair.pdf"))
PC_df$Pair = factor(PC_df$Pair,levels(PC_df$Pair)[order(dplyr::filter(PC_df, SampleType == "M")$PC2)])
pca <- ggplot(PC_df, aes(Pair, PC2))
pca + geom_point(size = 2, aes(colour = Pair)) + ggtitle("PCA paired")
# #ggsave(paste(pairedDirectory, "PCA_by_pair_2.pdf"))
Variance explained by each PCA:
summary(pr.out)
## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6
## Standard deviation 2.0863 1.3810 1.1638 1.02325 0.89607 0.75204
## Proportion of Variance 0.3549 0.1555 0.1104 0.08537 0.06547 0.04612
## Cumulative Proportion 0.3549 0.5104 0.6208 0.70621 0.77168 0.81780
## PC7 PC8 PC9 PC10 PC11 PC12
## Standard deviation 0.65190 0.53559 0.51752 0.47490 0.44968 0.40364
## Proportion of Variance 0.03465 0.02339 0.02184 0.01839 0.01649 0.01328
## Cumulative Proportion 0.85245 0.87584 0.89768 0.91607 0.93256 0.94584
## PC13 PC14 PC15 PC16 PC17 PC18
## Standard deviation 0.35476 0.3520 0.3341 0.29966 0.29328 0.27401
## Proportion of Variance 0.01026 0.0101 0.0091 0.00732 0.00701 0.00612
## Cumulative Proportion 0.95611 0.9662 0.9753 0.98264 0.98965 0.99577
## PC19 PC20
## Standard deviation 0.22775 1.546e-15
## Proportion of Variance 0.00423 0.000e+00
## Cumulative Proportion 1.00000 1.000e+00
Loadings of PC1 (highest 10):
print(sort(loadings1, decreasing = TRUE)[1:10])
## Cocktail.Intermediate_monocytes_STAT1
## 0.1992966
## Cocktail.Classical_monocytes_STAT1
## 0.1976372
## Cocktail.cDCs_STAT1
## 0.1934434
## Cocktail.CD56lo_NK_cells_STAT1
## 0.1875193
## Cocktail.MDSCs_STAT1
## 0.1756623
## Cocktail.CD56hi_NK_cells_STAT1
## 0.1745569
## Unstim.Nonclassical_monocytes_ERK
## 0.1744094
## Unstim.Nonclassical_monocytes_MAPKAPK2
## 0.1480448
## Cocktail.Tregs_STAT1
## 0.1461109
## Unstim.Nonclassical_monocytes_STAT1
## 0.1419455
Loadings of PC2 (highest 10):
print(sort(loadings2, decreasing = TRUE)[1:10])
## Cocktail.CD56lo_NK_cells_STAT1 LPS.pDCs_p38
## 0.17059745 0.16769165
## Cocktail.Tregs_STAT1 Cocktail.CD56hi_NK_cells_STAT1
## 0.15066615 0.11878973
## Cocktail.Classical_monocytes_STAT1 Unstim.Classical_monocytes_S6
## 0.11667543 0.11598467
## Cocktail.cDCs_STAT1 Unstim.cDCs_S6
## 0.11521778 0.11119839
## Cocktail.gd_T_cells_STAT1 Cocktail.CD4_T_cells_STAT1
## 0.10436562 0.09789317
The basal condition reflects what is occuring at steady state (versus stimulated). We additionally have the stimulated conditions (LPS and Cocktail).
dfs <- list("LPS" = LPS_df, "Cocktail" = Cocktail_df, "Unstim" = Unstim_df)
neonatal_SAM <- function(dfs, y, resp.type, SAMDirectory){
output <- list()
for (i in 1:length(dfs)){
df <- dfs[[i]]
x <- df[,!(names(df) %in% annotation_columns)]
sink("/dev/null")
model <- SAM(t(x), y, genenames = colnames(x), resp.type = resp.type, nperms = 1000, fdr.output = 0.01)
sink()
sig.up <- model$siggenes.table$genes.up[model$siggenes.table$genes.up[,"q-value(%)"] == "0", ]
sig.lo <- model$siggenes.table$genes.lo[model$siggenes.table$genes.lo[,"q-value(%)"] == "0", ]
sigs <- rbind(sig.up, sig.lo)
# write.csv(sigs, file = paste(SAMDirectory, names(dfs)[i], "_fdr_0.01.csv", sep = ""))
output[[names(dfs)[i]]] <- sigs
sig_df <- data.frame(sigs)
feat_vals <- cbind(Individual = df$Individual, df[, colnames(df) %in% sig_df$Gene.ID])
# write.csv(feat_vals, file = paste(SAMDirectory, names(dfs)[i], "_feature_values_fdr_0.01.csv", sep = ""))
df <- melt(df)
df <- df[df[, "variable"] %in% sig_df$Gene.ID,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle(names(dfs)[i]) + coord_flip() + theme(axis.text = element_text(size = 5))
print(p)
# #ggsave(filename = paste(SAMDirectory, names(dfs)[i], "_sig_plot.pdf", sep = ""), width = 30, height = 20)
print(names(dfs)[i])
print("Higher in Mother")
print(sig.up[, "Gene ID"])
print("Higher in Baby")
print(sig.lo[, "Gene ID"])
}
return(output)
}
paired_output <- neonatal_SAM(dfs, y, resp.type = "Two class paired", SAMDirectory = "./SAM/")
## Using Individual, Pair, SampleType, Condition as id variables
## [1] "LPS"
## [1] "Higher in Mother"
## [1] "Granulocytes_MAPKAPK2" "Intermediate_monocytes_CREB"
## [3] "Granulocytes_NFkB" "cDCs_ERK"
## [5] "Granulocytes_p38" "Nonclassical_monocytes_S6"
## [7] "Th1_T_cells_IkB" "Classical_monocytes_ERK"
## [9] "Intermediate_monocytes_S6" "Memory_CD8_T_cells_S6"
## [11] "Granulocytes_STAT1" "Intermediate_monocytes_ERK"
## [13] "Th1_T_cells_STAT1" "Th1_T_cells_STAT5"
## [15] "Nonclassical_monocytes_CREB" "cDCs_MAPKAPK2"
## [17] "Th1_T_cells_STAT3" "Th1_T_cells_CREB"
## [19] "Classical_monocytes_MAPKAPK2" "CD56lo_NK_cells_CREB"
## [21] "Memory_CD8_T_cells_CREB" "B_cells_ERK"
## [23] "Th1_T_cells_ERK" "pDCs_S6"
## [25] "pDCs_ERK" "Memory_CD4_T_cells_p38"
## [27] "Tregs_STAT1" "Th1_T_cells_p38"
## [29] "CD56hi_NK_cells_CREB" "Granulocytes_CREB"
## [31] "Tregs_CREB" "Th1_T_cells_S6"
## [33] "CD56hi_NK_cells_ERK" "Th1_T_cells_MAPKAPK2"
## [35] "pDCs_STAT3" "Tregs_ERK"
## [37] "Tregs_p38" "cDCs_p38"
## [39] "B_cells_STAT5" "cDCs_CREB"
## [41] "Naive_CD4_T_cells_ERK" "Intermediate_monocytes_IkB"
## [1] "Higher in Baby"
## NULL
## Using Individual, Pair, SampleType, Condition as id variables
## [1] "Cocktail"
## [1] "Higher in Mother"
## [1] "Classical_monocytes_STAT1" "cDCs_STAT1"
## [3] "Tregs_STAT1" "CD56lo_NK_cells_STAT1"
## [5] "Naive_CD4_T_cells_STAT1" "CD4_T_cells_STAT1"
## [7] "CD56hi_NK_cells_STAT1" "Classical_monocytes_STAT3"
## [9] "cDCs_STAT3" "Intermediate_monocytes_STAT1"
## [11] "pDCs_STAT5" "Memory_CD4_T_cells_STAT1"
## [13] "gd_T_cells_STAT1" "MDSCs_STAT3"
## [15] "Intermediate_monocytes_CREB" "pDCs_STAT1"
## [17] "Granulocytes_STAT1" "pDCs_STAT3"
## [19] "Nonclassical_monocytes_STAT1" "Nonclassical_monocytes_S6"
## [21] "Naive_CD8_T_cells_STAT1" "CD56lo_NK_cells_STAT3"
## [23] "Memory_CD8_T_cells_CREB" "Intermediate_monocytes_STAT3"
## [25] "Intermediate_monocytes_S6" "MDSCs_STAT1"
## [27] "Nonclassical_monocytes_CREB" "B_cells_STAT1"
## [29] "CD56lo_NK_cells_S6" "Memory_CD8_T_cells_S6"
## [31] "Th1_T_cells_ERK" "pDCs_ERK"
## [33] "CD56lo_NK_cells_CREB" "Granulocytes_NFkB"
## [35] "CD56lo_NK_cells_ERK" "Granulocytes_p38"
## [1] "Higher in Baby"
## [1] "Naive_CD8_T_cells_STAT5" "Naive_CD4_T_cells_STAT5"
## [3] "Memory_CD8_T_cells_STAT3" "CD8_T_cells_STAT5"
## [5] "CD8_T_cells_STAT3" "CD4_T_cells_STAT5"
## [7] "gd_T_cells_STAT5" "Memory_CD4_T_cells_STAT5"
## [9] "Intermediate_monocytes_MAPKAPK2" "CD56hi_NK_cells_MAPKAPK2"
## [11] "gd_T_cells_STAT3"
## Using SampleType, Condition, Pair, Individual as id variables
## [1] "Unstim"
## [1] "Higher in Mother"
## [1] "Intermediate_monocytes_STAT1" "Naive_CD4_T_cells_IkB"
## [3] "Intermediate_monocytes_STAT5" "CD4_T_cells_IkB"
## [5] "pDCs_NFkB" "CD4_T_cells_STAT1"
## [7] "Naive_CD4_T_cells_STAT1" "Nonclassical_monocytes_STAT5"
## [9] "Naive_CD8_T_cells_IkB" "Nonclassical_monocytes_STAT1"
## [11] "Intermediate_monocytes_p38" "Memory_CD4_T_cells_STAT1"
## [13] "Tregs_STAT1" "Intermediate_monocytes_MAPKAPK2"
## [15] "Naive_CD4_T_cells_STAT5" "CD4_T_cells_STAT5"
## [17] "Memory_CD4_T_cells_IkB" "Memory_CD4_T_cells_STAT5"
## [19] "gd_T_cells_STAT1" "Intermediate_monocytes_ERK"
## [21] "Naive_CD8_T_cells_STAT1" "Nonclassical_monocytes_p38"
## [23] "Tregs_NFkB" "pDCs_MAPKAPK2"
## [25] "Memory_CD4_T_cells_NFkB" "Nonclassical_monocytes_IkB"
## [27] "Nonclassical_monocytes_MAPKAPK2" "cDCs_STAT5"
## [29] "cDCs_STAT1" "CD56lo_NK_cells_STAT1"
## [31] "CD8_T_cells_STAT1" "Tregs_STAT5"
## [33] "pDCs_STAT1" "Classical_monocytes_STAT5"
## [35] "Classical_monocytes_STAT1" "Nonclassical_monocytes_ERK"
## [37] "pDCs_p38" "Naive_CD8_T_cells_STAT5"
## [1] "Higher in Baby"
## [1] "Memory_CD8_T_cells_MAPKAPK2" "B_cells_ERK"
## [3] "Memory_CD4_T_cells_MAPKAPK2" "Th1_T_cells_CREB"
## [5] "Th1_T_cells_S6" "Naive_CD8_T_cells_ERK"
## [7] "CD8_T_cells_ERK" "Tregs_S6"
## [9] "Th1_T_cells_MAPKAPK2" "CD8_T_cells_MAPKAPK2"
## [11] "gd_T_cells_MAPKAPK2" "B_cells_S6"
## [13] "CD4_T_cells_MAPKAPK2" "CD56lo_NK_cells_S6"
## [15] "Th1_T_cells_ERK" "CD56hi_NK_cells_IkB"
## [17] "B_cells_NFkB" "Tregs_MAPKAPK2"
## [19] "Memory_CD8_T_cells_ERK" "CD56lo_NK_cells_CREB"
## [21] "B_cells_STAT5" "Naive_CD4_T_cells_MAPKAPK2"
## [23] "Naive_CD4_T_cells_ERK" "Naive_CD8_T_cells_MAPKAPK2"
## [25] "Th1_T_cells_STAT3" "B_cells_MAPKAPK2"
## [27] "CD56hi_NK_cells_MAPKAPK2" "Tregs_CREB"
## [29] "CD4_T_cells_S6" "CD4_T_cells_ERK"
## [31] "B_cells_CREB" "Naive_CD8_T_cells_CREB"
## [33] "Naive_CD4_T_cells_CREB" "CD56hi_NK_cells_S6"
## [35] "Granulocytes_MAPKAPK2" "CD56hi_NK_cells_ERK"
## [37] "Th1_T_cells_STAT5" "CD56hi_NK_cells_CREB"
## [39] "Memory_CD4_T_cells_S6" "Memory_CD4_T_cells_ERK"
## [41] "Memory_CD8_T_cells_STAT5" "Th1_T_cells_IkB"
## [43] "Memory_CD4_T_cells_CREB" "Memory_CD8_T_cells_IkB"
## [45] "CD4_T_cells_CREB" "Naive_CD4_T_cells_S6"
## [47] "Granulocytes_CREB" "CD56lo_NK_cells_IkB"
## [49] "Th1_T_cells_STAT1" "MDSCs_CREB"
## [51] "cDCs_CREB" "Nonclassical_monocytes_S6"
For both stimulation conditions, there are many hits, and we may want to highlight a few based on effect size. Each stimulation has a different effect size. Here we plot all the means of the significant features in the LPS condition:
sig_LPS <- LPS_df[, colnames(LPS_df) %in% paired_output$LPS[, "Gene ID"] ]
means <- apply(sig_LPS, 2, mean)
plot(sort(means), main = "LPS significant means, sorted")
# pdf(paste(figure_directory, "LPS_sorted_abs_all.pdf", sep = ""),width = 6,height = 4, useDingbats=FALSE)
plot(sort(abs(means)), main = "LPS significant means, sorted", pch = 20)
abline(a = 0.1, b = 0, col = "red", lwd = 2)
dev.off()
## null device
## 1
Therefore if we set a cutoff of an induction of 0.1, we filter out the near-zero conditions and return the following features:
sig_feat_thresholded <- names(means[abs(means) > 0.1])
df <- melt(LPS_df)
## Using Individual, Pair, SampleType, Condition as id variables
df <- df[df[, "variable"] %in% sig_feat_thresholded,]
ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("LPS thresholded") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
# #ggsave(paste(figure_directory, "LPS_high_in_mom.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)
print(sig_feat_thresholded)
## [1] "Granulocytes_CREB" "Granulocytes_p38"
## [3] "Granulocytes_STAT1" "Granulocytes_MAPKAPK2"
## [5] "Granulocytes_NFkB" "Classical_monocytes_MAPKAPK2"
## [7] "Classical_monocytes_ERK" "Nonclassical_monocytes_CREB"
## [9] "Nonclassical_monocytes_S6" "cDCs_CREB"
## [11] "cDCs_p38" "cDCs_MAPKAPK2"
## [13] "cDCs_ERK" "pDCs_S6"
## [15] "Intermediate_monocytes_CREB" "Intermediate_monocytes_S6"
## [17] "Intermediate_monocytes_IkB" "Intermediate_monocytes_ERK"
# write.csv(sig_feat_thresholded, file = "~/Documents/neonatal/for_brice/LPS_SAM_higher_in_mom.csv")
All of these tend to be myeloid cells (Granulocytes, Monocyte subsets, DC subsets) signaling in MAPAKPK2, P38, CREB, ERK, S6, STAT1, IkB/NFkB. In addition, all of these are higher in mom (meaning mom has a higher innate immune signaling capacity than baby by our measurements).
We similarly can plot the Cocktail feature means to see the magnitude of induction:
df <- Cocktail_df
sig_feats <- df[, colnames(df) %in% paired_output$Cocktail[, "Gene ID"] ]
means <- apply(sig_feats, 2, mean)
plot(sort(means), main = "Cocktail significant means, sorted")
#pdf(paste(figure_directory, "Cocktail_sorted.pdf", sep = ""),width = 6,height = 4, useDingbats=FALSE)
#plot(sort(means), main = "Cocktail significant means, sorted", pch = 20)
#abline(a = 1, b = 0, col = "red", lwd = 2)
#dev.off()
Here we see a break point at arcsinh ratio of 1.0. We can filter there and get the following:
sig_feat_thresholded <- names(means[abs(means) > 1])
df <- melt(Cocktail_df)
## Using Individual, Pair, SampleType, Condition as id variables
df <- df[df[, "variable"] %in% sig_feat_thresholded,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Cocktail") + coord_flip() + theme(axis.text = element_text(size = 5))
print(p)
print(sig_feat_thresholded)
## [1] "Granulocytes_STAT1" "CD8_T_cells_STAT5"
## [3] "CD8_T_cells_STAT3" "CD4_T_cells_STAT5"
## [5] "CD4_T_cells_STAT1" "Naive_CD4_T_cells_STAT5"
## [7] "Naive_CD4_T_cells_STAT1" "Naive_CD8_T_cells_STAT5"
## [9] "Naive_CD8_T_cells_STAT1" "Memory_CD8_T_cells_STAT3"
## [11] "B_cells_STAT1" "Classical_monocytes_STAT1"
## [13] "Classical_monocytes_STAT3" "Nonclassical_monocytes_STAT1"
## [15] "cDCs_STAT1" "cDCs_STAT3"
## [17] "pDCs_STAT5" "pDCs_STAT1"
## [19] "pDCs_STAT3" "Intermediate_monocytes_STAT1"
## [21] "Intermediate_monocytes_STAT3" "MDSCs_STAT1"
## [23] "MDSCs_STAT3" "Tregs_STAT1"
## [25] "CD56lo_NK_cells_STAT1" "CD56lo_NK_cells_STAT3"
## [27] "CD56hi_NK_cells_STAT1" "gd_T_cells_STAT5"
## [29] "gd_T_cells_STAT1" "gd_T_cells_STAT3"
## [31] "Memory_CD4_T_cells_STAT5" "Memory_CD4_T_cells_STAT1"
This is list now contains a variety of both innate and adaptive cell types but all are pSTAT1, pSTAT3, and pSTAT5 signaling. Here’s if we look at only what’s higher in mom v. only what’s higher in baby:
m <- dplyr::filter(df, SampleType == "M")
m_by <- dplyr::group_by(m, variable)
m_mean <- summarise(m_by, mean_val = mean(value))
b <- dplyr::filter(df, SampleType == "B")
b_by <- dplyr::group_by(b, variable)
b_mean <- summarise(b_by, mean_val = mean(value))
# higher in mother
m_df <- m_mean$variable[m_mean$mean_val > b_mean$mean_val]
# write.csv(m_df, file = "~/Documents/neonatal/for_brice/Cocktail_SAM_higher_in_mom.csv")
df <- melt(Cocktail_df)
## Using Individual, Pair, SampleType, Condition as id variables
df <- df[df[, "variable"] %in% m_df,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Cocktail, thresholded, higher in mother") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)
# #ggsave(paste(figure_directory, "Cocktail_high_in_mom.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)
# higher in baby
b_df <- m_mean$variable[m_mean$mean_val < b_mean$mean_val]
# write.csv(b_df, file = "~/Documents/neonatal/for_brice/Cocktail_SAM_higher_in_baby.csv")
df <- melt(Cocktail_df)
## Using Individual, Pair, SampleType, Condition as id variables
df <- df[df[, "variable"] %in% b_df,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Cocktail, thresholded, higher in baby") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)
# #ggsave(paste(figure_directory, "Cocktail_high_in_baby.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)
It looks like all of the higher in baby are adaptive features, whereas most of the higher in mom and innate features.
In this case we do not have an induction over baseline, therefore to examine the significant features we order them by the size of the difference between mom and baby:
df <- Unstim_df
sig_feats <- df[, colnames(df) %in% paired_output$Unstim[, "Gene ID"] ]
sig_feats[["SampleType"]] <- Unstim_df$SampleType
M_feats <- sig_feats %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-SampleType)
B_feats <- sig_feats %>% dplyr::filter(SampleType == "B") %>% dplyr::select(-SampleType)
M_means <- apply(M_feats, 2, mean)
B_means <- apply(B_feats, 2, mean)
Diff_means <- M_means - B_means
# plot(sort(Diff_means), main = "Mean differences in unstimulated")
plot(sort(abs(Diff_means)), main = "Mean differences in unstimulated (absolute value)")
Here we use a cut of 0.3 in magnitude based on where the slope changes:
#pdf(paste(figure_directory, "Unstim_sorted.pdf", sep = ""),width = 6,height = 4, useDingbats=FALSE)
#plot(sort(abs(Diff_means)), main = "Mean differences in unstimulated (absolute value)", pch = 20)
#abline(a = 0.3, b = 0, col = "red", lwd = 2)
#dev.off()
sig_feat_thresholded <- names(Diff_means[abs(Diff_means) > 0.3])
df <- melt(Unstim_df)
## Using SampleType, Condition, Pair, Individual as id variables
df <- df[df[, "variable"] %in% sig_feat_thresholded,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Unstim_thresholded") + coord_flip() + theme(axis.text = element_text(size = 5))
print(p)
print(sig_feat_thresholded)
## [1] "CD8_T_cells_MAPKAPK2" "CD8_T_cells_ERK"
## [3] "Naive_CD8_T_cells_ERK" "Memory_CD8_T_cells_MAPKAPK2"
## [5] "B_cells_S6" "B_cells_ERK"
## [7] "Nonclassical_monocytes_STAT1" "Nonclassical_monocytes_MAPKAPK2"
## [9] "Nonclassical_monocytes_ERK" "Th1_T_cells_CREB"
## [11] "Th1_T_cells_S6" "Th1_T_cells_MAPKAPK2"
## [13] "Th1_T_cells_ERK" "Intermediate_monocytes_STAT1"
## [15] "Intermediate_monocytes_ERK" "CD56lo_NK_cells_CREB"
Here we can also split into higher in mom v. higher in baby (Unstim):
df <- df[df[, "variable"] %in% sig_feat_thresholded,]
m <- dplyr::filter(df, SampleType == "M")
m_by <- dplyr::group_by(m, variable)
m_mean <- summarise(m_by, mean_val = mean(value))
b <- dplyr::filter(df, SampleType == "B")
b_by <- dplyr::group_by(b, variable)
b_mean <- summarise(b_by, mean_val = mean(value))
# higher in mother
m_df <- m_mean$variable[m_mean$mean_val > b_mean$mean_val]
# write.csv(m_df, file = "~/Documents/neonatal/for_brice/Unstim_SAM_higher_in_mom.csv")
df <- melt(Unstim_df)
## Using SampleType, Condition, Pair, Individual as id variables
df <- df[df[, "variable"] %in% m_df,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Unstim, thresholded, higher in mother") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)
# #ggsave(paste(figure_directory, "Unstim_high_in_mother.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)
# higher in baby
b_df <- m_mean$variable[m_mean$mean_val < b_mean$mean_val]
# write.csv(b_df, file = "~/Documents/neonatal/for_brice/Unstim_SAM_higher_in_baby.csv")
df <- melt(Unstim_df)
## Using SampleType, Condition, Pair, Individual as id variables
df <- df[df[, "variable"] %in% b_df,]
p <- ggplot(df, aes(variable, value)) + geom_boxplot(aes(colour = SampleType)) + ggtitle("Unstim, thresholded, higher in baby") + coord_flip() + theme(axis.text = element_text(size = 5)) + scale_color_brewer(palette = "Dark2") + theme_bw()
print(p)
# #ggsave(paste(figure_directory, "Unstim_high_in_baby.pdf", sep = ""), width = 10, height = 10, useDingbats=FALSE)
## Using Individual, Pair, SampleType, Condition as id variables
## [1] "LPS"
## [1] "Higher in Mother"
## [1] "cDCs_ERK" "Intermediate_monocytes_CREB"
## [3] "Classical_monocytes_ERK" "Granulocytes_MAPKAPK2"
## [5] "Th1_T_cells_IkB" "Granulocytes_NFkB"
## [7] "cDCs_MAPKAPK2" "Th1_T_cells_STAT1"
## [9] "Th1_T_cells_STAT5" "Classical_monocytes_MAPKAPK2"
## [11] "Nonclassical_monocytes_S6" "Intermediate_monocytes_ERK"
## [13] "Th1_T_cells_ERK" "B_cells_ERK"
## [15] "Granulocytes_p38" "CD56lo_NK_cells_CREB"
## [17] "Granulocytes_STAT1" "Intermediate_monocytes_S6"
## [19] "Th1_T_cells_STAT3" "Th1_T_cells_CREB"
## [21] "Memory_CD8_T_cells_S6" "Tregs_STAT1"
## [23] "pDCs_S6" "Th1_T_cells_p38"
## [25] "Memory_CD4_T_cells_p38" "Memory_CD8_T_cells_CREB"
## [27] "Tregs_CREB" "Tregs_p38"
## [29] "pDCs_STAT3" "Th1_T_cells_MAPKAPK2"
## [31] "Th1_T_cells_S6" "B_cells_STAT5"
## [33] "CD56hi_NK_cells_ERK" "Tregs_ERK"
## [35] "Intermediate_monocytes_STAT3" "pDCs_ERK"
## [37] "CD56hi_NK_cells_CREB" "Naive_CD4_T_cells_ERK"
## [39] "Memory_CD8_T_cells_p38" "Nonclassical_monocytes_CREB"
## [41] "pDCs_CREB" "Granulocytes_CREB"
## [43] "Naive_CD4_T_cells_IkB" "cDCs_S6"
## [45] "Naive_CD8_T_cells_IkB" "Memory_CD4_T_cells_STAT1"
## [47] "cDCs_CREB" "gd_T_cells_S6"
## [49] "CD56lo_NK_cells_STAT1" "B_cells_S6"
## [1] "Higher in Baby"
## NULL
## Using Individual, Pair, SampleType, Condition as id variables
## [1] "Cocktail"
## [1] "Higher in Mother"
## [1] "Classical_monocytes_STAT1" "cDCs_STAT1"
## [3] "CD56lo_NK_cells_STAT1" "CD56hi_NK_cells_STAT1"
## [5] "Naive_CD4_T_cells_STAT1" "Classical_monocytes_STAT3"
## [7] "Intermediate_monocytes_STAT1" "Tregs_STAT1"
## [9] "cDCs_STAT3" "CD4_T_cells_STAT1"
## [11] "Memory_CD8_T_cells_CREB" "pDCs_STAT1"
## [13] "pDCs_STAT5" "Intermediate_monocytes_CREB"
## [15] "Intermediate_monocytes_STAT3" "MDSCs_STAT3"
## [17] "Memory_CD4_T_cells_STAT1" "gd_T_cells_STAT1"
## [19] "pDCs_STAT3" "Nonclassical_monocytes_CREB"
## [21] "MDSCs_STAT1" "Granulocytes_STAT1"
## [23] "Naive_CD8_T_cells_STAT1" "Nonclassical_monocytes_S6"
## [25] "CD56lo_NK_cells_STAT3" "Memory_CD8_T_cells_S6"
## [27] "Th1_T_cells_ERK" "Intermediate_monocytes_S6"
## [29] "CD56lo_NK_cells_CREB" "Granulocytes_NFkB"
## [31] "pDCs_ERK" "gd_T_cells_CREB"
## [33] "B_cells_STAT1"
## [1] "Higher in Baby"
## [1] "Naive_CD4_T_cells_STAT5" "Naive_CD8_T_cells_STAT5"
## [3] "CD8_T_cells_STAT5" "CD4_T_cells_STAT5"
## [5] "Memory_CD8_T_cells_STAT3" "Memory_CD4_T_cells_STAT5"
## [7] "gd_T_cells_STAT5" "CD56hi_NK_cells_MAPKAPK2"
## [9] "Intermediate_monocytes_MAPKAPK2" "CD8_T_cells_STAT3"
## Using SampleType, Condition, Pair, Individual as id variables
## [1] "Unstim"
## [1] "Higher in Mother"
## [1] "Intermediate_monocytes_STAT1" "Intermediate_monocytes_STAT5"
## [3] "Naive_CD4_T_cells_STAT5" "CD4_T_cells_STAT5"
## [5] "pDCs_NFkB" "Memory_CD4_T_cells_STAT5"
## [7] "Naive_CD4_T_cells_IkB" "Intermediate_monocytes_ERK"
## [9] "pDCs_STAT1" "Nonclassical_monocytes_STAT1"
## [11] "Intermediate_monocytes_p38" "Tregs_STAT1"
## [13] "cDCs_STAT5" "CD4_T_cells_STAT1"
## [15] "Naive_CD4_T_cells_STAT1" "Classical_monocytes_STAT5"
## [17] "gd_T_cells_STAT1" "Nonclassical_monocytes_STAT5"
## [19] "Memory_CD4_T_cells_STAT1" "Intermediate_monocytes_MAPKAPK2"
## [21] "Naive_CD8_T_cells_IkB" "cDCs_STAT1"
## [23] "CD4_T_cells_IkB" "Nonclassical_monocytes_p38"
## [25] "Classical_monocytes_STAT1" "Naive_CD8_T_cells_STAT1"
## [27] "Tregs_STAT5" "pDCs_p38"
## [29] "Naive_CD8_T_cells_STAT5" "CD56lo_NK_cells_STAT1"
## [31] "Tregs_NFkB"
## [1] "Higher in Baby"
## [1] "B_cells_ERK" "Th1_T_cells_CREB"
## [3] "Memory_CD8_T_cells_MAPKAPK2" "CD56lo_NK_cells_CREB"
## [5] "CD8_T_cells_ERK" "Naive_CD8_T_cells_ERK"
## [7] "Th1_T_cells_S6" "Th1_T_cells_MAPKAPK2"
## [9] "Th1_T_cells_ERK" "B_cells_S6"
## [11] "Memory_CD8_T_cells_ERK" "gd_T_cells_MAPKAPK2"
## [13] "CD8_T_cells_MAPKAPK2" "Naive_CD4_T_cells_ERK"
## [15] "CD56hi_NK_cells_CREB" "B_cells_CREB"
## [17] "Th1_T_cells_STAT3" "Memory_CD4_T_cells_MAPKAPK2"
## [19] "CD56lo_NK_cells_S6" "Tregs_S6"
## [21] "Tregs_CREB" "Naive_CD8_T_cells_CREB"
## [23] "CD4_T_cells_ERK" "Granulocytes_MAPKAPK2"
## [25] "CD56hi_NK_cells_IkB" "B_cells_NFkB"
## [27] "B_cells_STAT5" "Naive_CD4_T_cells_CREB"
## [29] "Th1_T_cells_STAT5" "CD56hi_NK_cells_ERK"
## [31] "MDSCs_CREB" "B_cells_MAPKAPK2"
## [33] "Granulocytes_CREB" "CD4_T_cells_MAPKAPK2"
## [35] "Memory_CD4_T_cells_ERK" "Tregs_MAPKAPK2"
## [37] "CD56hi_NK_cells_MAPKAPK2" "Naive_CD8_T_cells_MAPKAPK2"
## [39] "cDCs_CREB" "Th1_T_cells_IkB"
## [41] "CD56hi_NK_cells_S6" "Memory_CD4_T_cells_CREB"
## [43] "Memory_CD8_T_cells_STAT5"
Here we examine the added value of having paired samples (samples from a mother-baby pair as opposed to a random sample) by comparing the p-values from unpaired v. paired t-tests.
New Here we also compare to doing the significance cutoff as whether SAM paired v. unpaired found it as significant. We should use SAM throughout Here’s when we do it with all the signaling data combined (original analysis: Unstim, Cocktail, LPS)
# a function to calculate significance from SAM output
SAM_significance <- function(paired_output, unpaired_output, unpaired_pvals){
get_genes <- function(output){
all_genes <- c()
for (i in 1:length(output)){
genes <- output[[i]][, "Gene ID"]
gene_names <- paste(names(output)[i], genes, sep = ".")
all_genes <- c(all_genes, gene_names)
}
return(all_genes)
}
sig_paired <- get_genes(paired_output)
print(sig_paired)
sig_unpaired <- get_genes(unpaired_output)
print(sig_unpaired)
yes_p <- names(unpaired_pvals) %in% sig_paired
print(yes_p)
yes_up <- names(unpaired_pvals) %in% sig_unpaired
print(yes_up)
significance <- vector(mode = "character", length = length(unpaired_pvals))
significance[yes_p & yes_up] <- "Both"
significance[!(yes_p) & yes_up] <- "Unpaired only"
significance[yes_p & !(yes_up)] <- "Paired only"
significance[!(yes_p) & !(yes_up)] <- "Not significant"
return(significance)
}
# pairedDirectory <- "~/Documents/neonatal/paired/"
sampleType <- Unstim_df$SampleType
plot_p_v_up <- function(dfs, sampleType, paired_output, unpaired_output){
df <- do.call(cbind, args = dfs)
df[["SampleType"]] <- sampleType
mom_df <- df %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-contains("Individual"), -contains("Pair"), - contains("SampleType"), -contains("Condition"))
baby_df <- df %>% dplyr::filter(SampleType == "B") %>% dplyr::select(-contains("Individual"), -contains("Pair"), - contains("SampleType"), -contains("Condition"))
paired_pvals <- mapply(function(x, y) t.test(x,y, paired = TRUE)$p.value, mom_df, baby_df)
unpaired_pvals <- mapply(function(x, y) t.test(x,y, paired = FALSE)$p.value, mom_df, baby_df)
# plot(-log(unpaired_pvals), -log(paired_pvals))
# Number of comparisons: 20 cell types x 10 phosphos x 3 conditions
bonf <- .05/(ncol(mom_df))
significance <- vector(mode = "character", length = length(unpaired_pvals))
significance[(unpaired_pvals < bonf) & (paired_pvals < bonf)] <- "Both"
significance[(unpaired_pvals < bonf) & (paired_pvals > bonf)] <- "Unpaired only"
significance[(unpaired_pvals > bonf) & (paired_pvals < bonf)] <- "Paired only"
significance[(unpaired_pvals > bonf) & (paired_pvals > bonf)] <- "Not significant"
Significance_SAM <- SAM_significance(paired_output, unpaired_output, unpaired_pvals)
plot_df <- data.frame(unpaired_pvals, paired_pvals, Significance_Bonferroni = significance, Significance_SAM = Significance_SAM, Features = names(paired_pvals))
p <- ggplot(plot_df, aes(-log(unpaired_pvals), -log(paired_pvals))) +
geom_point(size = 1, aes(colour = Significance_Bonferroni)) +
scale_color_manual(values=c("blue", " dark gray", "red", "orange"))
print(p)
p <- ggplot(plot_df, aes(-log(unpaired_pvals), -log(paired_pvals))) +
geom_point(size = 1, aes(colour = Significance_SAM)) +
scale_color_manual(values=c("#1b9e77", " dark gray", "#7570b3", "#d95f02")) + ggtitle("Using SAM Significance") + theme_bw()
print(p)
# (paste(figure_directory, "scatter_paired_v_unpaired.pdf", sep = ""), width = 8, height = 7,useDingbats=FALSE)
# #ggsave(paste(pairedDirectory, "scatter_paired_unpaired.pdf", sep = ""))
# plot_df %>% dplyr::filter(Significance_SAM != "Not significant") %>%
# dplyr::select(-unpaired_pvals) %>%
# dplyr::select(-paired_pvals)
return(plot_df)
}
plot_df <- plot_p_v_up(dfs = list("LPS" = LPS_df, "Cocktail" = Cocktail_df, "Unstim" = Unstim_df), sampleType = sampleType, paired_output, unpaired_output)
## [1] "LPS.Granulocytes_MAPKAPK2"
## [2] "LPS.Intermediate_monocytes_CREB"
## [3] "LPS.Granulocytes_NFkB"
## [4] "LPS.cDCs_ERK"
## [5] "LPS.Granulocytes_p38"
## [6] "LPS.Nonclassical_monocytes_S6"
## [7] "LPS.Th1_T_cells_IkB"
## [8] "LPS.Classical_monocytes_ERK"
## [9] "LPS.Intermediate_monocytes_S6"
## [10] "LPS.Memory_CD8_T_cells_S6"
## [11] "LPS.Granulocytes_STAT1"
## [12] "LPS.Intermediate_monocytes_ERK"
## [13] "LPS.Th1_T_cells_STAT1"
## [14] "LPS.Th1_T_cells_STAT5"
## [15] "LPS.Nonclassical_monocytes_CREB"
## [16] "LPS.cDCs_MAPKAPK2"
## [17] "LPS.Th1_T_cells_STAT3"
## [18] "LPS.Th1_T_cells_CREB"
## [19] "LPS.Classical_monocytes_MAPKAPK2"
## [20] "LPS.CD56lo_NK_cells_CREB"
## [21] "LPS.Memory_CD8_T_cells_CREB"
## [22] "LPS.B_cells_ERK"
## [23] "LPS.Th1_T_cells_ERK"
## [24] "LPS.pDCs_S6"
## [25] "LPS.pDCs_ERK"
## [26] "LPS.Memory_CD4_T_cells_p38"
## [27] "LPS.Tregs_STAT1"
## [28] "LPS.Th1_T_cells_p38"
## [29] "LPS.CD56hi_NK_cells_CREB"
## [30] "LPS.Granulocytes_CREB"
## [31] "LPS.Tregs_CREB"
## [32] "LPS.Th1_T_cells_S6"
## [33] "LPS.CD56hi_NK_cells_ERK"
## [34] "LPS.Th1_T_cells_MAPKAPK2"
## [35] "LPS.pDCs_STAT3"
## [36] "LPS.Tregs_ERK"
## [37] "LPS.Tregs_p38"
## [38] "LPS.cDCs_p38"
## [39] "LPS.B_cells_STAT5"
## [40] "LPS.cDCs_CREB"
## [41] "LPS.Naive_CD4_T_cells_ERK"
## [42] "LPS.Intermediate_monocytes_IkB"
## [43] "Cocktail.Classical_monocytes_STAT1"
## [44] "Cocktail.cDCs_STAT1"
## [45] "Cocktail.Tregs_STAT1"
## [46] "Cocktail.CD56lo_NK_cells_STAT1"
## [47] "Cocktail.Naive_CD4_T_cells_STAT1"
## [48] "Cocktail.CD4_T_cells_STAT1"
## [49] "Cocktail.CD56hi_NK_cells_STAT1"
## [50] "Cocktail.Classical_monocytes_STAT3"
## [51] "Cocktail.cDCs_STAT3"
## [52] "Cocktail.Intermediate_monocytes_STAT1"
## [53] "Cocktail.pDCs_STAT5"
## [54] "Cocktail.Memory_CD4_T_cells_STAT1"
## [55] "Cocktail.gd_T_cells_STAT1"
## [56] "Cocktail.MDSCs_STAT3"
## [57] "Cocktail.Intermediate_monocytes_CREB"
## [58] "Cocktail.pDCs_STAT1"
## [59] "Cocktail.Granulocytes_STAT1"
## [60] "Cocktail.pDCs_STAT3"
## [61] "Cocktail.Nonclassical_monocytes_STAT1"
## [62] "Cocktail.Nonclassical_monocytes_S6"
## [63] "Cocktail.Naive_CD8_T_cells_STAT1"
## [64] "Cocktail.CD56lo_NK_cells_STAT3"
## [65] "Cocktail.Memory_CD8_T_cells_CREB"
## [66] "Cocktail.Intermediate_monocytes_STAT3"
## [67] "Cocktail.Intermediate_monocytes_S6"
## [68] "Cocktail.MDSCs_STAT1"
## [69] "Cocktail.Nonclassical_monocytes_CREB"
## [70] "Cocktail.B_cells_STAT1"
## [71] "Cocktail.CD56lo_NK_cells_S6"
## [72] "Cocktail.Memory_CD8_T_cells_S6"
## [73] "Cocktail.Th1_T_cells_ERK"
## [74] "Cocktail.pDCs_ERK"
## [75] "Cocktail.CD56lo_NK_cells_CREB"
## [76] "Cocktail.Granulocytes_NFkB"
## [77] "Cocktail.CD56lo_NK_cells_ERK"
## [78] "Cocktail.Granulocytes_p38"
## [79] "Cocktail.Naive_CD8_T_cells_STAT5"
## [80] "Cocktail.Naive_CD4_T_cells_STAT5"
## [81] "Cocktail.Memory_CD8_T_cells_STAT3"
## [82] "Cocktail.CD8_T_cells_STAT5"
## [83] "Cocktail.CD8_T_cells_STAT3"
## [84] "Cocktail.CD4_T_cells_STAT5"
## [85] "Cocktail.gd_T_cells_STAT5"
## [86] "Cocktail.Memory_CD4_T_cells_STAT5"
## [87] "Cocktail.Intermediate_monocytes_MAPKAPK2"
## [88] "Cocktail.CD56hi_NK_cells_MAPKAPK2"
## [89] "Cocktail.gd_T_cells_STAT3"
## [90] "Unstim.Intermediate_monocytes_STAT1"
## [91] "Unstim.Naive_CD4_T_cells_IkB"
## [92] "Unstim.Intermediate_monocytes_STAT5"
## [93] "Unstim.CD4_T_cells_IkB"
## [94] "Unstim.pDCs_NFkB"
## [95] "Unstim.CD4_T_cells_STAT1"
## [96] "Unstim.Naive_CD4_T_cells_STAT1"
## [97] "Unstim.Nonclassical_monocytes_STAT5"
## [98] "Unstim.Naive_CD8_T_cells_IkB"
## [99] "Unstim.Nonclassical_monocytes_STAT1"
## [100] "Unstim.Intermediate_monocytes_p38"
## [101] "Unstim.Memory_CD4_T_cells_STAT1"
## [102] "Unstim.Tregs_STAT1"
## [103] "Unstim.Intermediate_monocytes_MAPKAPK2"
## [104] "Unstim.Naive_CD4_T_cells_STAT5"
## [105] "Unstim.CD4_T_cells_STAT5"
## [106] "Unstim.Memory_CD4_T_cells_IkB"
## [107] "Unstim.Memory_CD4_T_cells_STAT5"
## [108] "Unstim.gd_T_cells_STAT1"
## [109] "Unstim.Intermediate_monocytes_ERK"
## [110] "Unstim.Naive_CD8_T_cells_STAT1"
## [111] "Unstim.Nonclassical_monocytes_p38"
## [112] "Unstim.Tregs_NFkB"
## [113] "Unstim.pDCs_MAPKAPK2"
## [114] "Unstim.Memory_CD4_T_cells_NFkB"
## [115] "Unstim.Nonclassical_monocytes_IkB"
## [116] "Unstim.Nonclassical_monocytes_MAPKAPK2"
## [117] "Unstim.cDCs_STAT5"
## [118] "Unstim.cDCs_STAT1"
## [119] "Unstim.CD56lo_NK_cells_STAT1"
## [120] "Unstim.CD8_T_cells_STAT1"
## [121] "Unstim.Tregs_STAT5"
## [122] "Unstim.pDCs_STAT1"
## [123] "Unstim.Classical_monocytes_STAT5"
## [124] "Unstim.Classical_monocytes_STAT1"
## [125] "Unstim.Nonclassical_monocytes_ERK"
## [126] "Unstim.pDCs_p38"
## [127] "Unstim.Naive_CD8_T_cells_STAT5"
## [128] "Unstim.Memory_CD8_T_cells_MAPKAPK2"
## [129] "Unstim.B_cells_ERK"
## [130] "Unstim.Memory_CD4_T_cells_MAPKAPK2"
## [131] "Unstim.Th1_T_cells_CREB"
## [132] "Unstim.Th1_T_cells_S6"
## [133] "Unstim.Naive_CD8_T_cells_ERK"
## [134] "Unstim.CD8_T_cells_ERK"
## [135] "Unstim.Tregs_S6"
## [136] "Unstim.Th1_T_cells_MAPKAPK2"
## [137] "Unstim.CD8_T_cells_MAPKAPK2"
## [138] "Unstim.gd_T_cells_MAPKAPK2"
## [139] "Unstim.B_cells_S6"
## [140] "Unstim.CD4_T_cells_MAPKAPK2"
## [141] "Unstim.CD56lo_NK_cells_S6"
## [142] "Unstim.Th1_T_cells_ERK"
## [143] "Unstim.CD56hi_NK_cells_IkB"
## [144] "Unstim.B_cells_NFkB"
## [145] "Unstim.Tregs_MAPKAPK2"
## [146] "Unstim.Memory_CD8_T_cells_ERK"
## [147] "Unstim.CD56lo_NK_cells_CREB"
## [148] "Unstim.B_cells_STAT5"
## [149] "Unstim.Naive_CD4_T_cells_MAPKAPK2"
## [150] "Unstim.Naive_CD4_T_cells_ERK"
## [151] "Unstim.Naive_CD8_T_cells_MAPKAPK2"
## [152] "Unstim.Th1_T_cells_STAT3"
## [153] "Unstim.B_cells_MAPKAPK2"
## [154] "Unstim.CD56hi_NK_cells_MAPKAPK2"
## [155] "Unstim.Tregs_CREB"
## [156] "Unstim.CD4_T_cells_S6"
## [157] "Unstim.CD4_T_cells_ERK"
## [158] "Unstim.B_cells_CREB"
## [159] "Unstim.Naive_CD8_T_cells_CREB"
## [160] "Unstim.Naive_CD4_T_cells_CREB"
## [161] "Unstim.CD56hi_NK_cells_S6"
## [162] "Unstim.Granulocytes_MAPKAPK2"
## [163] "Unstim.CD56hi_NK_cells_ERK"
## [164] "Unstim.Th1_T_cells_STAT5"
## [165] "Unstim.CD56hi_NK_cells_CREB"
## [166] "Unstim.Memory_CD4_T_cells_S6"
## [167] "Unstim.Memory_CD4_T_cells_ERK"
## [168] "Unstim.Memory_CD8_T_cells_STAT5"
## [169] "Unstim.Th1_T_cells_IkB"
## [170] "Unstim.Memory_CD4_T_cells_CREB"
## [171] "Unstim.Memory_CD8_T_cells_IkB"
## [172] "Unstim.CD4_T_cells_CREB"
## [173] "Unstim.Naive_CD4_T_cells_S6"
## [174] "Unstim.Granulocytes_CREB"
## [175] "Unstim.CD56lo_NK_cells_IkB"
## [176] "Unstim.Th1_T_cells_STAT1"
## [177] "Unstim.MDSCs_CREB"
## [178] "Unstim.cDCs_CREB"
## [179] "Unstim.Nonclassical_monocytes_S6"
## [1] "LPS.cDCs_ERK"
## [2] "LPS.Intermediate_monocytes_CREB"
## [3] "LPS.Classical_monocytes_ERK"
## [4] "LPS.Granulocytes_MAPKAPK2"
## [5] "LPS.Th1_T_cells_IkB"
## [6] "LPS.Granulocytes_NFkB"
## [7] "LPS.cDCs_MAPKAPK2"
## [8] "LPS.Th1_T_cells_STAT1"
## [9] "LPS.Th1_T_cells_STAT5"
## [10] "LPS.Classical_monocytes_MAPKAPK2"
## [11] "LPS.Nonclassical_monocytes_S6"
## [12] "LPS.Intermediate_monocytes_ERK"
## [13] "LPS.Th1_T_cells_ERK"
## [14] "LPS.B_cells_ERK"
## [15] "LPS.Granulocytes_p38"
## [16] "LPS.CD56lo_NK_cells_CREB"
## [17] "LPS.Granulocytes_STAT1"
## [18] "LPS.Intermediate_monocytes_S6"
## [19] "LPS.Th1_T_cells_STAT3"
## [20] "LPS.Th1_T_cells_CREB"
## [21] "LPS.Memory_CD8_T_cells_S6"
## [22] "LPS.Tregs_STAT1"
## [23] "LPS.pDCs_S6"
## [24] "LPS.Th1_T_cells_p38"
## [25] "LPS.Memory_CD4_T_cells_p38"
## [26] "LPS.Memory_CD8_T_cells_CREB"
## [27] "LPS.Tregs_CREB"
## [28] "LPS.Tregs_p38"
## [29] "LPS.pDCs_STAT3"
## [30] "LPS.Th1_T_cells_MAPKAPK2"
## [31] "LPS.Th1_T_cells_S6"
## [32] "LPS.B_cells_STAT5"
## [33] "LPS.CD56hi_NK_cells_ERK"
## [34] "LPS.Tregs_ERK"
## [35] "LPS.Intermediate_monocytes_STAT3"
## [36] "LPS.pDCs_ERK"
## [37] "LPS.CD56hi_NK_cells_CREB"
## [38] "LPS.Naive_CD4_T_cells_ERK"
## [39] "LPS.Memory_CD8_T_cells_p38"
## [40] "LPS.Nonclassical_monocytes_CREB"
## [41] "LPS.pDCs_CREB"
## [42] "LPS.Granulocytes_CREB"
## [43] "LPS.Naive_CD4_T_cells_IkB"
## [44] "LPS.cDCs_S6"
## [45] "LPS.Naive_CD8_T_cells_IkB"
## [46] "LPS.Memory_CD4_T_cells_STAT1"
## [47] "LPS.cDCs_CREB"
## [48] "LPS.gd_T_cells_S6"
## [49] "LPS.CD56lo_NK_cells_STAT1"
## [50] "LPS.B_cells_S6"
## [51] "Cocktail.Classical_monocytes_STAT1"
## [52] "Cocktail.cDCs_STAT1"
## [53] "Cocktail.CD56lo_NK_cells_STAT1"
## [54] "Cocktail.CD56hi_NK_cells_STAT1"
## [55] "Cocktail.Naive_CD4_T_cells_STAT1"
## [56] "Cocktail.Classical_monocytes_STAT3"
## [57] "Cocktail.Intermediate_monocytes_STAT1"
## [58] "Cocktail.Tregs_STAT1"
## [59] "Cocktail.cDCs_STAT3"
## [60] "Cocktail.CD4_T_cells_STAT1"
## [61] "Cocktail.Memory_CD8_T_cells_CREB"
## [62] "Cocktail.pDCs_STAT1"
## [63] "Cocktail.pDCs_STAT5"
## [64] "Cocktail.Intermediate_monocytes_CREB"
## [65] "Cocktail.Intermediate_monocytes_STAT3"
## [66] "Cocktail.MDSCs_STAT3"
## [67] "Cocktail.Memory_CD4_T_cells_STAT1"
## [68] "Cocktail.gd_T_cells_STAT1"
## [69] "Cocktail.pDCs_STAT3"
## [70] "Cocktail.Nonclassical_monocytes_CREB"
## [71] "Cocktail.MDSCs_STAT1"
## [72] "Cocktail.Granulocytes_STAT1"
## [73] "Cocktail.Naive_CD8_T_cells_STAT1"
## [74] "Cocktail.Nonclassical_monocytes_S6"
## [75] "Cocktail.CD56lo_NK_cells_STAT3"
## [76] "Cocktail.Memory_CD8_T_cells_S6"
## [77] "Cocktail.Th1_T_cells_ERK"
## [78] "Cocktail.Intermediate_monocytes_S6"
## [79] "Cocktail.CD56lo_NK_cells_CREB"
## [80] "Cocktail.Granulocytes_NFkB"
## [81] "Cocktail.pDCs_ERK"
## [82] "Cocktail.gd_T_cells_CREB"
## [83] "Cocktail.B_cells_STAT1"
## [84] "Cocktail.Naive_CD4_T_cells_STAT5"
## [85] "Cocktail.Naive_CD8_T_cells_STAT5"
## [86] "Cocktail.CD8_T_cells_STAT5"
## [87] "Cocktail.CD4_T_cells_STAT5"
## [88] "Cocktail.Memory_CD8_T_cells_STAT3"
## [89] "Cocktail.Memory_CD4_T_cells_STAT5"
## [90] "Cocktail.gd_T_cells_STAT5"
## [91] "Cocktail.CD56hi_NK_cells_MAPKAPK2"
## [92] "Cocktail.Intermediate_monocytes_MAPKAPK2"
## [93] "Cocktail.CD8_T_cells_STAT3"
## [94] "Unstim.Intermediate_monocytes_STAT1"
## [95] "Unstim.Intermediate_monocytes_STAT5"
## [96] "Unstim.Naive_CD4_T_cells_STAT5"
## [97] "Unstim.CD4_T_cells_STAT5"
## [98] "Unstim.pDCs_NFkB"
## [99] "Unstim.Memory_CD4_T_cells_STAT5"
## [100] "Unstim.Naive_CD4_T_cells_IkB"
## [101] "Unstim.Intermediate_monocytes_ERK"
## [102] "Unstim.pDCs_STAT1"
## [103] "Unstim.Nonclassical_monocytes_STAT1"
## [104] "Unstim.Intermediate_monocytes_p38"
## [105] "Unstim.Tregs_STAT1"
## [106] "Unstim.cDCs_STAT5"
## [107] "Unstim.CD4_T_cells_STAT1"
## [108] "Unstim.Naive_CD4_T_cells_STAT1"
## [109] "Unstim.Classical_monocytes_STAT5"
## [110] "Unstim.gd_T_cells_STAT1"
## [111] "Unstim.Nonclassical_monocytes_STAT5"
## [112] "Unstim.Memory_CD4_T_cells_STAT1"
## [113] "Unstim.Intermediate_monocytes_MAPKAPK2"
## [114] "Unstim.Naive_CD8_T_cells_IkB"
## [115] "Unstim.cDCs_STAT1"
## [116] "Unstim.CD4_T_cells_IkB"
## [117] "Unstim.Nonclassical_monocytes_p38"
## [118] "Unstim.Classical_monocytes_STAT1"
## [119] "Unstim.Naive_CD8_T_cells_STAT1"
## [120] "Unstim.Tregs_STAT5"
## [121] "Unstim.pDCs_p38"
## [122] "Unstim.Naive_CD8_T_cells_STAT5"
## [123] "Unstim.CD56lo_NK_cells_STAT1"
## [124] "Unstim.Tregs_NFkB"
## [125] "Unstim.B_cells_ERK"
## [126] "Unstim.Th1_T_cells_CREB"
## [127] "Unstim.Memory_CD8_T_cells_MAPKAPK2"
## [128] "Unstim.CD56lo_NK_cells_CREB"
## [129] "Unstim.CD8_T_cells_ERK"
## [130] "Unstim.Naive_CD8_T_cells_ERK"
## [131] "Unstim.Th1_T_cells_S6"
## [132] "Unstim.Th1_T_cells_MAPKAPK2"
## [133] "Unstim.Th1_T_cells_ERK"
## [134] "Unstim.B_cells_S6"
## [135] "Unstim.Memory_CD8_T_cells_ERK"
## [136] "Unstim.gd_T_cells_MAPKAPK2"
## [137] "Unstim.CD8_T_cells_MAPKAPK2"
## [138] "Unstim.Naive_CD4_T_cells_ERK"
## [139] "Unstim.CD56hi_NK_cells_CREB"
## [140] "Unstim.B_cells_CREB"
## [141] "Unstim.Th1_T_cells_STAT3"
## [142] "Unstim.Memory_CD4_T_cells_MAPKAPK2"
## [143] "Unstim.CD56lo_NK_cells_S6"
## [144] "Unstim.Tregs_S6"
## [145] "Unstim.Tregs_CREB"
## [146] "Unstim.Naive_CD8_T_cells_CREB"
## [147] "Unstim.CD4_T_cells_ERK"
## [148] "Unstim.Granulocytes_MAPKAPK2"
## [149] "Unstim.CD56hi_NK_cells_IkB"
## [150] "Unstim.B_cells_NFkB"
## [151] "Unstim.B_cells_STAT5"
## [152] "Unstim.Naive_CD4_T_cells_CREB"
## [153] "Unstim.Th1_T_cells_STAT5"
## [154] "Unstim.CD56hi_NK_cells_ERK"
## [155] "Unstim.MDSCs_CREB"
## [156] "Unstim.B_cells_MAPKAPK2"
## [157] "Unstim.Granulocytes_CREB"
## [158] "Unstim.CD4_T_cells_MAPKAPK2"
## [159] "Unstim.Memory_CD4_T_cells_ERK"
## [160] "Unstim.Tregs_MAPKAPK2"
## [161] "Unstim.CD56hi_NK_cells_MAPKAPK2"
## [162] "Unstim.Naive_CD8_T_cells_MAPKAPK2"
## [163] "Unstim.cDCs_CREB"
## [164] "Unstim.Th1_T_cells_IkB"
## [165] "Unstim.CD56hi_NK_cells_S6"
## [166] "Unstim.Memory_CD4_T_cells_CREB"
## [167] "Unstim.Memory_CD8_T_cells_STAT5"
## [1] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE
## [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [34] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [45] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [56] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [67] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [78] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
## [89] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [100] TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE
## [111] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
## [122] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [144] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE
## [199] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE
## [243] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [265] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
## [276] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE
## [298] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [342] FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [353] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
## [364] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [386] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
## [397] TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE
## [408] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE
## [419] FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE
## [430] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE
## [441] TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE
## [452] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [463] TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE
## [474] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
## [485] FALSE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE
## [496] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE
## [507] TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [518] FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE
## [529] TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE
## [540] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE
## [551] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE
## [562] TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE
## [1] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE
## [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [34] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE
## [45] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE
## [56] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE
## [67] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [78] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
## [89] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE
## [100] TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE
## [111] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
## [122] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [144] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [199] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE
## [243] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [265] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [276] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE
## [298] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [342] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [353] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE
## [364] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [386] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [397] TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE
## [408] TRUE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE
## [419] FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE
## [430] TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE
## [441] TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE
## [452] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [463] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
## [474] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
## [485] FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE
## [496] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE
## [507] TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [518] FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE
## [529] TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
## [540] FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE
## [551] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE
## [562] TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE
test <- strsplit(as.character(plot_df$Features), "[.]")
plot_df_new <- data.frame(plot_df, Condition = sapply(test, function(x) x[[1]]))
levels(plot_df_new$Condition) <- c(levels(plot_df_new$Condition), "Not Significant")
plot_df_new[plot_df_new$Significance_SAM == "Not significant", "Condition"] <- "Not Significant"
ggplot(plot_df_new, aes(-log(unpaired_pvals), -log(paired_pvals))) +
geom_point(size = 1, aes(colour = Condition)) +
scale_color_manual(values=c("#1b9e77", "#d95f02", "#7570b3", "dark grey")) + ggtitle("Colored by condition") + theme_bw()
# #ggsave(paste(figure_directory, "scatter_by_stim.pdf"), width = 8, height = 7, useDingbats=FALSE)
Here’s for Unstim only:
plot_p_v_up(dfs = list("Unstim" = Unstim_df), sampleType = sampleType, paired_output = list("Unstim" = paired_output$Unstim), unpaired_output = list("Unstim" = unpaired_output$Unstim))
## [1] "Unstim.Intermediate_monocytes_STAT1"
## [2] "Unstim.Naive_CD4_T_cells_IkB"
## [3] "Unstim.Intermediate_monocytes_STAT5"
## [4] "Unstim.CD4_T_cells_IkB"
## [5] "Unstim.pDCs_NFkB"
## [6] "Unstim.CD4_T_cells_STAT1"
## [7] "Unstim.Naive_CD4_T_cells_STAT1"
## [8] "Unstim.Nonclassical_monocytes_STAT5"
## [9] "Unstim.Naive_CD8_T_cells_IkB"
## [10] "Unstim.Nonclassical_monocytes_STAT1"
## [11] "Unstim.Intermediate_monocytes_p38"
## [12] "Unstim.Memory_CD4_T_cells_STAT1"
## [13] "Unstim.Tregs_STAT1"
## [14] "Unstim.Intermediate_monocytes_MAPKAPK2"
## [15] "Unstim.Naive_CD4_T_cells_STAT5"
## [16] "Unstim.CD4_T_cells_STAT5"
## [17] "Unstim.Memory_CD4_T_cells_IkB"
## [18] "Unstim.Memory_CD4_T_cells_STAT5"
## [19] "Unstim.gd_T_cells_STAT1"
## [20] "Unstim.Intermediate_monocytes_ERK"
## [21] "Unstim.Naive_CD8_T_cells_STAT1"
## [22] "Unstim.Nonclassical_monocytes_p38"
## [23] "Unstim.Tregs_NFkB"
## [24] "Unstim.pDCs_MAPKAPK2"
## [25] "Unstim.Memory_CD4_T_cells_NFkB"
## [26] "Unstim.Nonclassical_monocytes_IkB"
## [27] "Unstim.Nonclassical_monocytes_MAPKAPK2"
## [28] "Unstim.cDCs_STAT5"
## [29] "Unstim.cDCs_STAT1"
## [30] "Unstim.CD56lo_NK_cells_STAT1"
## [31] "Unstim.CD8_T_cells_STAT1"
## [32] "Unstim.Tregs_STAT5"
## [33] "Unstim.pDCs_STAT1"
## [34] "Unstim.Classical_monocytes_STAT5"
## [35] "Unstim.Classical_monocytes_STAT1"
## [36] "Unstim.Nonclassical_monocytes_ERK"
## [37] "Unstim.pDCs_p38"
## [38] "Unstim.Naive_CD8_T_cells_STAT5"
## [39] "Unstim.Memory_CD8_T_cells_MAPKAPK2"
## [40] "Unstim.B_cells_ERK"
## [41] "Unstim.Memory_CD4_T_cells_MAPKAPK2"
## [42] "Unstim.Th1_T_cells_CREB"
## [43] "Unstim.Th1_T_cells_S6"
## [44] "Unstim.Naive_CD8_T_cells_ERK"
## [45] "Unstim.CD8_T_cells_ERK"
## [46] "Unstim.Tregs_S6"
## [47] "Unstim.Th1_T_cells_MAPKAPK2"
## [48] "Unstim.CD8_T_cells_MAPKAPK2"
## [49] "Unstim.gd_T_cells_MAPKAPK2"
## [50] "Unstim.B_cells_S6"
## [51] "Unstim.CD4_T_cells_MAPKAPK2"
## [52] "Unstim.CD56lo_NK_cells_S6"
## [53] "Unstim.Th1_T_cells_ERK"
## [54] "Unstim.CD56hi_NK_cells_IkB"
## [55] "Unstim.B_cells_NFkB"
## [56] "Unstim.Tregs_MAPKAPK2"
## [57] "Unstim.Memory_CD8_T_cells_ERK"
## [58] "Unstim.CD56lo_NK_cells_CREB"
## [59] "Unstim.B_cells_STAT5"
## [60] "Unstim.Naive_CD4_T_cells_MAPKAPK2"
## [61] "Unstim.Naive_CD4_T_cells_ERK"
## [62] "Unstim.Naive_CD8_T_cells_MAPKAPK2"
## [63] "Unstim.Th1_T_cells_STAT3"
## [64] "Unstim.B_cells_MAPKAPK2"
## [65] "Unstim.CD56hi_NK_cells_MAPKAPK2"
## [66] "Unstim.Tregs_CREB"
## [67] "Unstim.CD4_T_cells_S6"
## [68] "Unstim.CD4_T_cells_ERK"
## [69] "Unstim.B_cells_CREB"
## [70] "Unstim.Naive_CD8_T_cells_CREB"
## [71] "Unstim.Naive_CD4_T_cells_CREB"
## [72] "Unstim.CD56hi_NK_cells_S6"
## [73] "Unstim.Granulocytes_MAPKAPK2"
## [74] "Unstim.CD56hi_NK_cells_ERK"
## [75] "Unstim.Th1_T_cells_STAT5"
## [76] "Unstim.CD56hi_NK_cells_CREB"
## [77] "Unstim.Memory_CD4_T_cells_S6"
## [78] "Unstim.Memory_CD4_T_cells_ERK"
## [79] "Unstim.Memory_CD8_T_cells_STAT5"
## [80] "Unstim.Th1_T_cells_IkB"
## [81] "Unstim.Memory_CD4_T_cells_CREB"
## [82] "Unstim.Memory_CD8_T_cells_IkB"
## [83] "Unstim.CD4_T_cells_CREB"
## [84] "Unstim.Naive_CD4_T_cells_S6"
## [85] "Unstim.Granulocytes_CREB"
## [86] "Unstim.CD56lo_NK_cells_IkB"
## [87] "Unstim.Th1_T_cells_STAT1"
## [88] "Unstim.MDSCs_CREB"
## [89] "Unstim.cDCs_CREB"
## [90] "Unstim.Nonclassical_monocytes_S6"
## [1] "Unstim.Intermediate_monocytes_STAT1"
## [2] "Unstim.Intermediate_monocytes_STAT5"
## [3] "Unstim.Naive_CD4_T_cells_STAT5"
## [4] "Unstim.CD4_T_cells_STAT5"
## [5] "Unstim.pDCs_NFkB"
## [6] "Unstim.Memory_CD4_T_cells_STAT5"
## [7] "Unstim.Naive_CD4_T_cells_IkB"
## [8] "Unstim.Intermediate_monocytes_ERK"
## [9] "Unstim.pDCs_STAT1"
## [10] "Unstim.Nonclassical_monocytes_STAT1"
## [11] "Unstim.Intermediate_monocytes_p38"
## [12] "Unstim.Tregs_STAT1"
## [13] "Unstim.cDCs_STAT5"
## [14] "Unstim.CD4_T_cells_STAT1"
## [15] "Unstim.Naive_CD4_T_cells_STAT1"
## [16] "Unstim.Classical_monocytes_STAT5"
## [17] "Unstim.gd_T_cells_STAT1"
## [18] "Unstim.Nonclassical_monocytes_STAT5"
## [19] "Unstim.Memory_CD4_T_cells_STAT1"
## [20] "Unstim.Intermediate_monocytes_MAPKAPK2"
## [21] "Unstim.Naive_CD8_T_cells_IkB"
## [22] "Unstim.cDCs_STAT1"
## [23] "Unstim.CD4_T_cells_IkB"
## [24] "Unstim.Nonclassical_monocytes_p38"
## [25] "Unstim.Classical_monocytes_STAT1"
## [26] "Unstim.Naive_CD8_T_cells_STAT1"
## [27] "Unstim.Tregs_STAT5"
## [28] "Unstim.pDCs_p38"
## [29] "Unstim.Naive_CD8_T_cells_STAT5"
## [30] "Unstim.CD56lo_NK_cells_STAT1"
## [31] "Unstim.Tregs_NFkB"
## [32] "Unstim.B_cells_ERK"
## [33] "Unstim.Th1_T_cells_CREB"
## [34] "Unstim.Memory_CD8_T_cells_MAPKAPK2"
## [35] "Unstim.CD56lo_NK_cells_CREB"
## [36] "Unstim.CD8_T_cells_ERK"
## [37] "Unstim.Naive_CD8_T_cells_ERK"
## [38] "Unstim.Th1_T_cells_S6"
## [39] "Unstim.Th1_T_cells_MAPKAPK2"
## [40] "Unstim.Th1_T_cells_ERK"
## [41] "Unstim.B_cells_S6"
## [42] "Unstim.Memory_CD8_T_cells_ERK"
## [43] "Unstim.gd_T_cells_MAPKAPK2"
## [44] "Unstim.CD8_T_cells_MAPKAPK2"
## [45] "Unstim.Naive_CD4_T_cells_ERK"
## [46] "Unstim.CD56hi_NK_cells_CREB"
## [47] "Unstim.B_cells_CREB"
## [48] "Unstim.Th1_T_cells_STAT3"
## [49] "Unstim.Memory_CD4_T_cells_MAPKAPK2"
## [50] "Unstim.CD56lo_NK_cells_S6"
## [51] "Unstim.Tregs_S6"
## [52] "Unstim.Tregs_CREB"
## [53] "Unstim.Naive_CD8_T_cells_CREB"
## [54] "Unstim.CD4_T_cells_ERK"
## [55] "Unstim.Granulocytes_MAPKAPK2"
## [56] "Unstim.CD56hi_NK_cells_IkB"
## [57] "Unstim.B_cells_NFkB"
## [58] "Unstim.B_cells_STAT5"
## [59] "Unstim.Naive_CD4_T_cells_CREB"
## [60] "Unstim.Th1_T_cells_STAT5"
## [61] "Unstim.CD56hi_NK_cells_ERK"
## [62] "Unstim.MDSCs_CREB"
## [63] "Unstim.B_cells_MAPKAPK2"
## [64] "Unstim.Granulocytes_CREB"
## [65] "Unstim.CD4_T_cells_MAPKAPK2"
## [66] "Unstim.Memory_CD4_T_cells_ERK"
## [67] "Unstim.Tregs_MAPKAPK2"
## [68] "Unstim.CD56hi_NK_cells_MAPKAPK2"
## [69] "Unstim.Naive_CD8_T_cells_MAPKAPK2"
## [70] "Unstim.cDCs_CREB"
## [71] "Unstim.Th1_T_cells_IkB"
## [72] "Unstim.CD56hi_NK_cells_S6"
## [73] "Unstim.Memory_CD4_T_cells_CREB"
## [74] "Unstim.Memory_CD8_T_cells_STAT5"
## [1] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [12] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE
## [23] FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE
## [34] TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE
## [45] FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
## [56] FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE
## [67] TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
## [78] FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE
## [89] FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
## [100] FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE
## [111] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE
## [122] TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
## [144] TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE
## [155] FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [166] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [177] TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE
## [188] TRUE TRUE TRUE
## [1] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [12] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE
## [23] FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE
## [34] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE
## [45] FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
## [56] FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE
## [67] TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
## [78] FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE
## [89] FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE
## [100] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
## [111] TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE
## [122] TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
## [144] TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE TRUE
## [155] FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [166] TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [177] TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE TRUE
## [188] FALSE FALSE TRUE
## unpaired_pvals paired_pvals
## Unstim.Granulocytes_CREB 1.454526e-02 1.766102e-02
## Unstim.Granulocytes_STAT5 3.202311e-01 3.277756e-01
## Unstim.Granulocytes_p38 1.245449e-01 8.248464e-02
## Unstim.Granulocytes_STAT1 6.426266e-01 5.630320e-01
## Unstim.Granulocytes_STAT3 4.620542e-01 4.622732e-01
## Unstim.Granulocytes_S6 6.413594e-01 4.921344e-01
## Unstim.Granulocytes_MAPKAPK2 2.772374e-03 2.676850e-03
## Unstim.Granulocytes_IkB 8.217323e-01 7.689908e-01
## Unstim.Granulocytes_NFkB 2.655910e-02 9.547049e-02
## Unstim.Granulocytes_ERK 6.914283e-01 6.393495e-01
## Unstim.CD8_T_cells_CREB 1.361972e-01 7.578972e-02
## Unstim.CD8_T_cells_STAT5 4.693152e-01 4.209354e-01
## Unstim.CD8_T_cells_p38 4.062352e-01 6.141304e-02
## Unstim.CD8_T_cells_STAT1 1.215706e-02 3.715064e-04
## Unstim.CD8_T_cells_STAT3 9.809138e-01 9.777724e-01
## Unstim.CD8_T_cells_S6 2.556543e-01 4.064876e-02
## Unstim.CD8_T_cells_MAPKAPK2 6.549684e-04 5.489678e-06
## Unstim.CD8_T_cells_IkB 6.203808e-01 4.167615e-01
## Unstim.CD8_T_cells_NFkB 3.241919e-01 1.012624e-02
## Unstim.CD8_T_cells_ERK 1.576608e-06 1.597554e-06
## Unstim.CD4_T_cells_CREB 1.026805e-02 5.247107e-03
## Unstim.CD4_T_cells_STAT5 2.590401e-04 4.102107e-04
## Unstim.CD4_T_cells_p38 7.276975e-02 4.219835e-03
## Unstim.CD4_T_cells_STAT1 3.579931e-04 2.324301e-05
## Unstim.CD4_T_cells_STAT3 3.697803e-01 3.395004e-01
## Unstim.CD4_T_cells_S6 2.311343e-02 1.194707e-04
## Unstim.CD4_T_cells_MAPKAPK2 1.232085e-02 8.268912e-07
## Unstim.CD4_T_cells_IkB 5.646785e-03 4.741550e-06
## Unstim.CD4_T_cells_NFkB 1.883986e-01 1.734440e-02
## Unstim.CD4_T_cells_ERK 1.718611e-03 6.638037e-04
## Unstim.Naive_CD4_T_cells_CREB 8.010365e-04 5.605928e-04
## Unstim.Naive_CD4_T_cells_STAT5 2.348562e-04 3.773025e-04
## Unstim.Naive_CD4_T_cells_p38 1.507699e-01 1.574535e-02
## Unstim.Naive_CD4_T_cells_STAT1 4.646169e-04 3.322016e-05
## Unstim.Naive_CD4_T_cells_STAT3 7.089910e-01 6.845043e-01
## Unstim.Naive_CD4_T_cells_S6 1.388757e-01 3.476053e-03
## Unstim.Naive_CD4_T_cells_MAPKAPK2 6.786987e-02 5.914279e-06
## Unstim.Naive_CD4_T_cells_IkB 6.495783e-04 7.691806e-07
## Unstim.Naive_CD4_T_cells_NFkB 8.945786e-01 7.670955e-01
## Unstim.Naive_CD4_T_cells_ERK 2.342420e-04 7.289549e-05
## Unstim.Naive_CD8_T_cells_CREB 1.645490e-03 1.348310e-03
## Unstim.Naive_CD8_T_cells_STAT5 9.294308e-03 8.910078e-03
## Unstim.Naive_CD8_T_cells_p38 2.050132e-01 1.702127e-02
## Unstim.Naive_CD8_T_cells_STAT1 1.345853e-03 8.396036e-05
## Unstim.Naive_CD8_T_cells_STAT3 3.428543e-01 3.008317e-01
## Unstim.Naive_CD8_T_cells_S6 3.548405e-01 3.966789e-02
## Unstim.Naive_CD8_T_cells_MAPKAPK2 1.887013e-02 5.267062e-05
## Unstim.Naive_CD8_T_cells_IkB 3.719079e-03 8.364752e-05
## Unstim.Naive_CD8_T_cells_NFkB 3.113698e-01 7.074941e-03
## Unstim.Naive_CD8_T_cells_ERK 1.108382e-06 1.140432e-06
## Unstim.Memory_CD8_T_cells_CREB 7.124438e-02 8.493809e-02
## Unstim.Memory_CD8_T_cells_STAT5 7.766084e-03 1.107976e-03
## Unstim.Memory_CD8_T_cells_p38 8.608828e-01 6.248965e-01
## Unstim.Memory_CD8_T_cells_STAT1 3.000903e-01 6.019463e-02
## Unstim.Memory_CD8_T_cells_STAT3 2.329910e-01 8.151749e-02
## Unstim.Memory_CD8_T_cells_S6 5.015557e-01 3.766946e-01
## Unstim.Memory_CD8_T_cells_MAPKAPK2 4.289447e-08 3.197727e-09
## Unstim.Memory_CD8_T_cells_IkB 7.489677e-02 4.747219e-03
## Unstim.Memory_CD8_T_cells_NFkB 1.902935e-01 1.361559e-02
## Unstim.Memory_CD8_T_cells_ERK 7.326216e-05 9.539203e-05
## Unstim.B_cells_CREB 4.699529e-04 1.488296e-03
## Unstim.B_cells_STAT5 4.282646e-04 3.213624e-06
## Unstim.B_cells_p38 8.608881e-01 7.707381e-01
## Unstim.B_cells_STAT1 1.420030e-01 1.325136e-02
## Unstim.B_cells_STAT3 1.314229e-01 3.268618e-03
## Unstim.B_cells_S6 1.374829e-04 2.028772e-05
## Unstim.B_cells_MAPKAPK2 6.119177e-03 8.396951e-05
## Unstim.B_cells_IkB 3.808809e-01 3.084587e-01
## Unstim.B_cells_NFkB 2.394253e-03 1.169341e-05
## Unstim.B_cells_ERK 2.394424e-10 7.661840e-09
## Unstim.Classical_monocytes_CREB 4.871372e-02 4.378973e-02
## Unstim.Classical_monocytes_STAT5 8.686032e-05 1.776084e-03
## Unstim.Classical_monocytes_p38 8.929760e-01 8.865349e-01
## Unstim.Classical_monocytes_STAT1 7.685218e-03 5.132992e-03
## Unstim.Classical_monocytes_STAT3 9.648935e-01 9.616188e-01
## Unstim.Classical_monocytes_S6 1.916912e-01 1.977249e-01
## Unstim.Classical_monocytes_MAPKAPK2 7.545863e-01 7.423764e-01
## Unstim.Classical_monocytes_IkB 2.488134e-01 1.626920e-01
## Unstim.Classical_monocytes_NFkB 8.359534e-01 8.042830e-01
## Unstim.Classical_monocytes_ERK 9.070471e-01 9.106081e-01
## Unstim.Nonclassical_monocytes_CREB 9.999437e-01 9.998882e-01
## Unstim.Nonclassical_monocytes_STAT5 2.500545e-03 8.649429e-05
## Unstim.Nonclassical_monocytes_p38 1.176526e-02 8.956742e-04
## Unstim.Nonclassical_monocytes_STAT1 3.540195e-03 3.854479e-04
## Unstim.Nonclassical_monocytes_STAT3 9.774740e-01 9.775543e-01
## Unstim.Nonclassical_monocytes_S6 1.201234e-01 1.970360e-02
## Unstim.Nonclassical_monocytes_MAPKAPK2 7.928352e-02 3.283031e-03
## Unstim.Nonclassical_monocytes_IkB 6.181633e-02 1.287460e-04
## Unstim.Nonclassical_monocytes_NFkB 2.223616e-01 8.091316e-02
## Unstim.Nonclassical_monocytes_ERK 8.497462e-02 1.099825e-02
## Unstim.cDCs_CREB 2.978829e-02 2.534888e-02
## Unstim.cDCs_STAT5 4.570719e-05 9.560468e-04
## Unstim.cDCs_p38 9.295080e-01 9.233575e-01
## Unstim.cDCs_STAT1 4.520671e-03 2.810899e-03
## Unstim.cDCs_STAT3 9.040712e-01 8.905688e-01
## Unstim.cDCs_S6 1.382516e-01 1.463724e-01
## Unstim.cDCs_MAPKAPK2 7.155604e-01 6.967120e-01
## Unstim.cDCs_IkB 7.160396e-01 5.943869e-01
## Unstim.cDCs_NFkB 8.253854e-01 7.951046e-01
## Unstim.cDCs_ERK 9.791583e-01 9.795998e-01
## Unstim.pDCs_CREB 1.680440e-01 7.024380e-02
## Unstim.pDCs_STAT5 8.745327e-03 3.705902e-02
## Unstim.pDCs_p38 4.055557e-03 3.329537e-03
## Unstim.pDCs_STAT1 1.019619e-03 5.428900e-03
## Unstim.pDCs_STAT3 9.602168e-01 9.570234e-01
## Unstim.pDCs_S6 9.781401e-01 9.597474e-01
## Unstim.pDCs_MAPKAPK2 3.577841e-02 4.503037e-05
## Unstim.pDCs_IkB 6.299101e-01 4.837252e-01
## Unstim.pDCs_NFkB 3.658271e-05 5.361157e-05
## Unstim.pDCs_ERK 2.813664e-01 2.307529e-01
## Unstim.Th1_T_cells_CREB 1.622506e-08 1.187629e-06
## Unstim.Th1_T_cells_STAT5 4.187996e-03 2.254899e-03
## Unstim.Th1_T_cells_p38 1.078065e-01 1.928383e-02
## Unstim.Th1_T_cells_STAT1 4.591208e-02 7.466226e-03
## Unstim.Th1_T_cells_STAT3 9.047198e-04 2.984681e-04
## Unstim.Th1_T_cells_S6 2.243662e-06 6.166400e-07
## Unstim.Th1_T_cells_MAPKAPK2 1.064577e-05 7.758919e-06
## Unstim.Th1_T_cells_IkB 2.656847e-02 5.335171e-03
## Unstim.Th1_T_cells_NFkB 4.380637e-01 3.406712e-01
## Unstim.Th1_T_cells_ERK 1.036898e-05 3.982343e-05
## Unstim.Intermediate_monocytes_CREB 2.368477e-01 6.276065e-02
## Unstim.Intermediate_monocytes_STAT5 1.708067e-06 1.013132e-06
## Unstim.Intermediate_monocytes_p38 1.536889e-03 1.901202e-04
## Unstim.Intermediate_monocytes_STAT1 6.182054e-07 4.919566e-07
## Unstim.Intermediate_monocytes_STAT3 6.530164e-01 6.034361e-01
## Unstim.Intermediate_monocytes_S6 8.796489e-01 8.056760e-01
## Unstim.Intermediate_monocytes_MAPKAPK2 5.797078e-03 2.812815e-04
## Unstim.Intermediate_monocytes_IkB 9.079383e-01 8.633441e-01
## Unstim.Intermediate_monocytes_NFkB 4.131249e-01 3.222873e-01
## Unstim.Intermediate_monocytes_ERK 3.400942e-03 1.063070e-03
## Unstim.MDSCs_CREB 1.431711e-02 2.406331e-02
## Unstim.MDSCs_STAT5 1.004589e-01 1.440341e-01
## Unstim.MDSCs_p38 9.262632e-01 9.291324e-01
## Unstim.MDSCs_STAT1 2.173736e-01 2.216592e-01
## Unstim.MDSCs_STAT3 4.273799e-01 4.050715e-01
## Unstim.MDSCs_S6 2.233628e-01 2.810726e-01
## Unstim.MDSCs_MAPKAPK2 1.063303e-01 1.174360e-01
## Unstim.MDSCs_IkB 2.891704e-01 1.468705e-01
## Unstim.MDSCs_NFkB 4.003107e-01 3.588322e-01
## Unstim.MDSCs_ERK 1.608174e-01 2.325880e-01
## Unstim.Tregs_CREB 1.849495e-04 2.831146e-04
## Unstim.Tregs_STAT5 3.411355e-03 1.863819e-03
## Unstim.Tregs_p38 1.429264e-01 4.069978e-02
## Unstim.Tregs_STAT1 1.080640e-04 1.976221e-05
## Unstim.Tregs_STAT3 4.669445e-01 4.346297e-01
## Unstim.Tregs_S6 4.661775e-04 3.916383e-07
## Unstim.Tregs_MAPKAPK2 7.297274e-03 4.975501e-06
## Unstim.Tregs_IkB 1.507385e-01 4.291098e-03
## Unstim.Tregs_NFkB 4.781831e-03 1.089386e-04
## Unstim.Tregs_ERK 1.231384e-01 5.786449e-02
## Unstim.CD56lo_NK_cells_CREB 2.469892e-06 1.965991e-04
## Unstim.CD56lo_NK_cells_STAT5 6.110157e-01 3.612637e-01
## Unstim.CD56lo_NK_cells_p38 1.093914e-01 4.941500e-02
## Unstim.CD56lo_NK_cells_STAT1 2.126306e-03 6.077802e-04
## Unstim.CD56lo_NK_cells_STAT3 7.280944e-02 1.386118e-03
## Unstim.CD56lo_NK_cells_S6 9.564652e-04 2.142184e-05
## Unstim.CD56lo_NK_cells_MAPKAPK2 2.854836e-01 2.691145e-02
## Unstim.CD56lo_NK_cells_IkB 4.065633e-02 4.839771e-03
## Unstim.CD56lo_NK_cells_NFkB 1.381510e-01 7.265945e-03
## Unstim.CD56lo_NK_cells_ERK 9.281219e-01 8.799194e-01
## Unstim.CD56hi_NK_cells_CREB 3.769450e-04 4.512660e-03
## Unstim.CD56hi_NK_cells_STAT5 2.902737e-01 1.693072e-01
## Unstim.CD56hi_NK_cells_p38 1.181669e-01 5.827460e-02
## Unstim.CD56hi_NK_cells_STAT1 9.078685e-03 1.343663e-02
## Unstim.CD56hi_NK_cells_STAT3 1.191327e-01 1.375071e-02
## Unstim.CD56hi_NK_cells_S6 2.178416e-02 1.711371e-03
## Unstim.CD56hi_NK_cells_MAPKAPK2 8.924476e-03 9.382232e-05
## Unstim.CD56hi_NK_cells_IkB 1.289271e-03 4.341278e-06
## Unstim.CD56hi_NK_cells_NFkB 4.803780e-02 2.360860e-02
## Unstim.CD56hi_NK_cells_ERK 3.493981e-03 1.853259e-03
## Unstim.gd_T_cells_CREB 2.792406e-01 3.672940e-01
## Unstim.gd_T_cells_STAT5 4.426911e-01 2.023715e-01
## Unstim.gd_T_cells_p38 3.108195e-02 9.858180e-04
## Unstim.gd_T_cells_STAT1 2.581577e-04 1.032419e-04
## Unstim.gd_T_cells_STAT3 5.905688e-01 3.602265e-01
## Unstim.gd_T_cells_S6 1.399920e-01 9.248786e-02
## Unstim.gd_T_cells_MAPKAPK2 1.276031e-04 2.605004e-06
## Unstim.gd_T_cells_IkB 8.358901e-01 8.083248e-01
## Unstim.gd_T_cells_NFkB 1.187126e-01 2.525241e-02
## Unstim.gd_T_cells_ERK 4.172333e-01 3.931471e-01
## Unstim.Memory_CD4_T_cells_CREB 9.327271e-03 3.514399e-03
## Unstim.Memory_CD4_T_cells_STAT5 3.419699e-04 3.839441e-04
## Unstim.Memory_CD4_T_cells_p38 4.586416e-02 1.075034e-03
## Unstim.Memory_CD4_T_cells_STAT1 6.122297e-04 2.640403e-05
## Unstim.Memory_CD4_T_cells_STAT3 1.496695e-01 1.265940e-01
## Unstim.Memory_CD4_T_cells_S6 1.399293e-02 7.575542e-04
## Unstim.Memory_CD4_T_cells_MAPKAPK2 6.188081e-04 2.574874e-08
## Unstim.Memory_CD4_T_cells_IkB 3.240368e-02 6.630191e-05
## Unstim.Memory_CD4_T_cells_NFkB 2.572740e-02 1.015704e-04
## Unstim.Memory_CD4_T_cells_ERK 6.959549e-03 2.236756e-03
## Significance_Bonferroni
## Unstim.Granulocytes_CREB Not significant
## Unstim.Granulocytes_STAT5 Not significant
## Unstim.Granulocytes_p38 Not significant
## Unstim.Granulocytes_STAT1 Not significant
## Unstim.Granulocytes_STAT3 Not significant
## Unstim.Granulocytes_S6 Not significant
## Unstim.Granulocytes_MAPKAPK2 Not significant
## Unstim.Granulocytes_IkB Not significant
## Unstim.Granulocytes_NFkB Not significant
## Unstim.Granulocytes_ERK Not significant
## Unstim.CD8_T_cells_CREB Not significant
## Unstim.CD8_T_cells_STAT5 Not significant
## Unstim.CD8_T_cells_p38 Not significant
## Unstim.CD8_T_cells_STAT1 Not significant
## Unstim.CD8_T_cells_STAT3 Not significant
## Unstim.CD8_T_cells_S6 Not significant
## Unstim.CD8_T_cells_MAPKAPK2 Paired only
## Unstim.CD8_T_cells_IkB Not significant
## Unstim.CD8_T_cells_NFkB Not significant
## Unstim.CD8_T_cells_ERK Both
## Unstim.CD4_T_cells_CREB Not significant
## Unstim.CD4_T_cells_STAT5 Unpaired only
## Unstim.CD4_T_cells_p38 Not significant
## Unstim.CD4_T_cells_STAT1 Paired only
## Unstim.CD4_T_cells_STAT3 Not significant
## Unstim.CD4_T_cells_S6 Paired only
## Unstim.CD4_T_cells_MAPKAPK2 Paired only
## Unstim.CD4_T_cells_IkB Paired only
## Unstim.CD4_T_cells_NFkB Not significant
## Unstim.CD4_T_cells_ERK Not significant
## Unstim.Naive_CD4_T_cells_CREB Not significant
## Unstim.Naive_CD4_T_cells_STAT5 Unpaired only
## Unstim.Naive_CD4_T_cells_p38 Not significant
## Unstim.Naive_CD4_T_cells_STAT1 Paired only
## Unstim.Naive_CD4_T_cells_STAT3 Not significant
## Unstim.Naive_CD4_T_cells_S6 Not significant
## Unstim.Naive_CD4_T_cells_MAPKAPK2 Paired only
## Unstim.Naive_CD4_T_cells_IkB Paired only
## Unstim.Naive_CD4_T_cells_NFkB Not significant
## Unstim.Naive_CD4_T_cells_ERK Both
## Unstim.Naive_CD8_T_cells_CREB Not significant
## Unstim.Naive_CD8_T_cells_STAT5 Not significant
## Unstim.Naive_CD8_T_cells_p38 Not significant
## Unstim.Naive_CD8_T_cells_STAT1 Paired only
## Unstim.Naive_CD8_T_cells_STAT3 Not significant
## Unstim.Naive_CD8_T_cells_S6 Not significant
## Unstim.Naive_CD8_T_cells_MAPKAPK2 Paired only
## Unstim.Naive_CD8_T_cells_IkB Paired only
## Unstim.Naive_CD8_T_cells_NFkB Not significant
## Unstim.Naive_CD8_T_cells_ERK Both
## Unstim.Memory_CD8_T_cells_CREB Not significant
## Unstim.Memory_CD8_T_cells_STAT5 Not significant
## Unstim.Memory_CD8_T_cells_p38 Not significant
## Unstim.Memory_CD8_T_cells_STAT1 Not significant
## Unstim.Memory_CD8_T_cells_STAT3 Not significant
## Unstim.Memory_CD8_T_cells_S6 Not significant
## Unstim.Memory_CD8_T_cells_MAPKAPK2 Both
## Unstim.Memory_CD8_T_cells_IkB Not significant
## Unstim.Memory_CD8_T_cells_NFkB Not significant
## Unstim.Memory_CD8_T_cells_ERK Both
## Unstim.B_cells_CREB Not significant
## Unstim.B_cells_STAT5 Paired only
## Unstim.B_cells_p38 Not significant
## Unstim.B_cells_STAT1 Not significant
## Unstim.B_cells_STAT3 Not significant
## Unstim.B_cells_S6 Both
## Unstim.B_cells_MAPKAPK2 Paired only
## Unstim.B_cells_IkB Not significant
## Unstim.B_cells_NFkB Paired only
## Unstim.B_cells_ERK Both
## Unstim.Classical_monocytes_CREB Not significant
## Unstim.Classical_monocytes_STAT5 Unpaired only
## Unstim.Classical_monocytes_p38 Not significant
## Unstim.Classical_monocytes_STAT1 Not significant
## Unstim.Classical_monocytes_STAT3 Not significant
## Unstim.Classical_monocytes_S6 Not significant
## Unstim.Classical_monocytes_MAPKAPK2 Not significant
## Unstim.Classical_monocytes_IkB Not significant
## Unstim.Classical_monocytes_NFkB Not significant
## Unstim.Classical_monocytes_ERK Not significant
## Unstim.Nonclassical_monocytes_CREB Not significant
## Unstim.Nonclassical_monocytes_STAT5 Paired only
## Unstim.Nonclassical_monocytes_p38 Not significant
## Unstim.Nonclassical_monocytes_STAT1 Not significant
## Unstim.Nonclassical_monocytes_STAT3 Not significant
## Unstim.Nonclassical_monocytes_S6 Not significant
## Unstim.Nonclassical_monocytes_MAPKAPK2 Not significant
## Unstim.Nonclassical_monocytes_IkB Paired only
## Unstim.Nonclassical_monocytes_NFkB Not significant
## Unstim.Nonclassical_monocytes_ERK Not significant
## Unstim.cDCs_CREB Not significant
## Unstim.cDCs_STAT5 Unpaired only
## Unstim.cDCs_p38 Not significant
## Unstim.cDCs_STAT1 Not significant
## Unstim.cDCs_STAT3 Not significant
## Unstim.cDCs_S6 Not significant
## Unstim.cDCs_MAPKAPK2 Not significant
## Unstim.cDCs_IkB Not significant
## Unstim.cDCs_NFkB Not significant
## Unstim.cDCs_ERK Not significant
## Unstim.pDCs_CREB Not significant
## Unstim.pDCs_STAT5 Not significant
## Unstim.pDCs_p38 Not significant
## Unstim.pDCs_STAT1 Not significant
## Unstim.pDCs_STAT3 Not significant
## Unstim.pDCs_S6 Not significant
## Unstim.pDCs_MAPKAPK2 Paired only
## Unstim.pDCs_IkB Not significant
## Unstim.pDCs_NFkB Both
## Unstim.pDCs_ERK Not significant
## Unstim.Th1_T_cells_CREB Both
## Unstim.Th1_T_cells_STAT5 Not significant
## Unstim.Th1_T_cells_p38 Not significant
## Unstim.Th1_T_cells_STAT1 Not significant
## Unstim.Th1_T_cells_STAT3 Not significant
## Unstim.Th1_T_cells_S6 Both
## Unstim.Th1_T_cells_MAPKAPK2 Both
## Unstim.Th1_T_cells_IkB Not significant
## Unstim.Th1_T_cells_NFkB Not significant
## Unstim.Th1_T_cells_ERK Both
## Unstim.Intermediate_monocytes_CREB Not significant
## Unstim.Intermediate_monocytes_STAT5 Both
## Unstim.Intermediate_monocytes_p38 Paired only
## Unstim.Intermediate_monocytes_STAT1 Both
## Unstim.Intermediate_monocytes_STAT3 Not significant
## Unstim.Intermediate_monocytes_S6 Not significant
## Unstim.Intermediate_monocytes_MAPKAPK2 Not significant
## Unstim.Intermediate_monocytes_IkB Not significant
## Unstim.Intermediate_monocytes_NFkB Not significant
## Unstim.Intermediate_monocytes_ERK Not significant
## Unstim.MDSCs_CREB Not significant
## Unstim.MDSCs_STAT5 Not significant
## Unstim.MDSCs_p38 Not significant
## Unstim.MDSCs_STAT1 Not significant
## Unstim.MDSCs_STAT3 Not significant
## Unstim.MDSCs_S6 Not significant
## Unstim.MDSCs_MAPKAPK2 Not significant
## Unstim.MDSCs_IkB Not significant
## Unstim.MDSCs_NFkB Not significant
## Unstim.MDSCs_ERK Not significant
## Unstim.Tregs_CREB Unpaired only
## Unstim.Tregs_STAT5 Not significant
## Unstim.Tregs_p38 Not significant
## Unstim.Tregs_STAT1 Both
## Unstim.Tregs_STAT3 Not significant
## Unstim.Tregs_S6 Paired only
## Unstim.Tregs_MAPKAPK2 Paired only
## Unstim.Tregs_IkB Not significant
## Unstim.Tregs_NFkB Paired only
## Unstim.Tregs_ERK Not significant
## Unstim.CD56lo_NK_cells_CREB Both
## Unstim.CD56lo_NK_cells_STAT5 Not significant
## Unstim.CD56lo_NK_cells_p38 Not significant
## Unstim.CD56lo_NK_cells_STAT1 Not significant
## Unstim.CD56lo_NK_cells_STAT3 Not significant
## Unstim.CD56lo_NK_cells_S6 Paired only
## Unstim.CD56lo_NK_cells_MAPKAPK2 Not significant
## Unstim.CD56lo_NK_cells_IkB Not significant
## Unstim.CD56lo_NK_cells_NFkB Not significant
## Unstim.CD56lo_NK_cells_ERK Not significant
## Unstim.CD56hi_NK_cells_CREB Not significant
## Unstim.CD56hi_NK_cells_STAT5 Not significant
## Unstim.CD56hi_NK_cells_p38 Not significant
## Unstim.CD56hi_NK_cells_STAT1 Not significant
## Unstim.CD56hi_NK_cells_STAT3 Not significant
## Unstim.CD56hi_NK_cells_S6 Not significant
## Unstim.CD56hi_NK_cells_MAPKAPK2 Paired only
## Unstim.CD56hi_NK_cells_IkB Paired only
## Unstim.CD56hi_NK_cells_NFkB Not significant
## Unstim.CD56hi_NK_cells_ERK Not significant
## Unstim.gd_T_cells_CREB Not significant
## Unstim.gd_T_cells_STAT5 Not significant
## Unstim.gd_T_cells_p38 Not significant
## Unstim.gd_T_cells_STAT1 Both
## Unstim.gd_T_cells_STAT3 Not significant
## Unstim.gd_T_cells_S6 Not significant
## Unstim.gd_T_cells_MAPKAPK2 Both
## Unstim.gd_T_cells_IkB Not significant
## Unstim.gd_T_cells_NFkB Not significant
## Unstim.gd_T_cells_ERK Not significant
## Unstim.Memory_CD4_T_cells_CREB Not significant
## Unstim.Memory_CD4_T_cells_STAT5 Not significant
## Unstim.Memory_CD4_T_cells_p38 Not significant
## Unstim.Memory_CD4_T_cells_STAT1 Paired only
## Unstim.Memory_CD4_T_cells_STAT3 Not significant
## Unstim.Memory_CD4_T_cells_S6 Not significant
## Unstim.Memory_CD4_T_cells_MAPKAPK2 Paired only
## Unstim.Memory_CD4_T_cells_IkB Paired only
## Unstim.Memory_CD4_T_cells_NFkB Paired only
## Unstim.Memory_CD4_T_cells_ERK Not significant
## Significance_SAM
## Unstim.Granulocytes_CREB Both
## Unstim.Granulocytes_STAT5 Not significant
## Unstim.Granulocytes_p38 Not significant
## Unstim.Granulocytes_STAT1 Not significant
## Unstim.Granulocytes_STAT3 Not significant
## Unstim.Granulocytes_S6 Not significant
## Unstim.Granulocytes_MAPKAPK2 Both
## Unstim.Granulocytes_IkB Not significant
## Unstim.Granulocytes_NFkB Not significant
## Unstim.Granulocytes_ERK Not significant
## Unstim.CD8_T_cells_CREB Not significant
## Unstim.CD8_T_cells_STAT5 Not significant
## Unstim.CD8_T_cells_p38 Not significant
## Unstim.CD8_T_cells_STAT1 Paired only
## Unstim.CD8_T_cells_STAT3 Not significant
## Unstim.CD8_T_cells_S6 Not significant
## Unstim.CD8_T_cells_MAPKAPK2 Both
## Unstim.CD8_T_cells_IkB Not significant
## Unstim.CD8_T_cells_NFkB Not significant
## Unstim.CD8_T_cells_ERK Both
## Unstim.CD4_T_cells_CREB Paired only
## Unstim.CD4_T_cells_STAT5 Both
## Unstim.CD4_T_cells_p38 Not significant
## Unstim.CD4_T_cells_STAT1 Both
## Unstim.CD4_T_cells_STAT3 Not significant
## Unstim.CD4_T_cells_S6 Paired only
## Unstim.CD4_T_cells_MAPKAPK2 Both
## Unstim.CD4_T_cells_IkB Both
## Unstim.CD4_T_cells_NFkB Not significant
## Unstim.CD4_T_cells_ERK Both
## Unstim.Naive_CD4_T_cells_CREB Both
## Unstim.Naive_CD4_T_cells_STAT5 Both
## Unstim.Naive_CD4_T_cells_p38 Not significant
## Unstim.Naive_CD4_T_cells_STAT1 Both
## Unstim.Naive_CD4_T_cells_STAT3 Not significant
## Unstim.Naive_CD4_T_cells_S6 Paired only
## Unstim.Naive_CD4_T_cells_MAPKAPK2 Paired only
## Unstim.Naive_CD4_T_cells_IkB Both
## Unstim.Naive_CD4_T_cells_NFkB Not significant
## Unstim.Naive_CD4_T_cells_ERK Both
## Unstim.Naive_CD8_T_cells_CREB Both
## Unstim.Naive_CD8_T_cells_STAT5 Both
## Unstim.Naive_CD8_T_cells_p38 Not significant
## Unstim.Naive_CD8_T_cells_STAT1 Both
## Unstim.Naive_CD8_T_cells_STAT3 Not significant
## Unstim.Naive_CD8_T_cells_S6 Not significant
## Unstim.Naive_CD8_T_cells_MAPKAPK2 Both
## Unstim.Naive_CD8_T_cells_IkB Both
## Unstim.Naive_CD8_T_cells_NFkB Not significant
## Unstim.Naive_CD8_T_cells_ERK Both
## Unstim.Memory_CD8_T_cells_CREB Not significant
## Unstim.Memory_CD8_T_cells_STAT5 Both
## Unstim.Memory_CD8_T_cells_p38 Not significant
## Unstim.Memory_CD8_T_cells_STAT1 Not significant
## Unstim.Memory_CD8_T_cells_STAT3 Not significant
## Unstim.Memory_CD8_T_cells_S6 Not significant
## Unstim.Memory_CD8_T_cells_MAPKAPK2 Both
## Unstim.Memory_CD8_T_cells_IkB Paired only
## Unstim.Memory_CD8_T_cells_NFkB Not significant
## Unstim.Memory_CD8_T_cells_ERK Both
## Unstim.B_cells_CREB Both
## Unstim.B_cells_STAT5 Both
## Unstim.B_cells_p38 Not significant
## Unstim.B_cells_STAT1 Not significant
## Unstim.B_cells_STAT3 Not significant
## Unstim.B_cells_S6 Both
## Unstim.B_cells_MAPKAPK2 Both
## Unstim.B_cells_IkB Not significant
## Unstim.B_cells_NFkB Both
## Unstim.B_cells_ERK Both
## Unstim.Classical_monocytes_CREB Not significant
## Unstim.Classical_monocytes_STAT5 Both
## Unstim.Classical_monocytes_p38 Not significant
## Unstim.Classical_monocytes_STAT1 Both
## Unstim.Classical_monocytes_STAT3 Not significant
## Unstim.Classical_monocytes_S6 Not significant
## Unstim.Classical_monocytes_MAPKAPK2 Not significant
## Unstim.Classical_monocytes_IkB Not significant
## Unstim.Classical_monocytes_NFkB Not significant
## Unstim.Classical_monocytes_ERK Not significant
## Unstim.Nonclassical_monocytes_CREB Not significant
## Unstim.Nonclassical_monocytes_STAT5 Both
## Unstim.Nonclassical_monocytes_p38 Both
## Unstim.Nonclassical_monocytes_STAT1 Both
## Unstim.Nonclassical_monocytes_STAT3 Not significant
## Unstim.Nonclassical_monocytes_S6 Paired only
## Unstim.Nonclassical_monocytes_MAPKAPK2 Paired only
## Unstim.Nonclassical_monocytes_IkB Paired only
## Unstim.Nonclassical_monocytes_NFkB Not significant
## Unstim.Nonclassical_monocytes_ERK Paired only
## Unstim.cDCs_CREB Both
## Unstim.cDCs_STAT5 Both
## Unstim.cDCs_p38 Not significant
## Unstim.cDCs_STAT1 Both
## Unstim.cDCs_STAT3 Not significant
## Unstim.cDCs_S6 Not significant
## Unstim.cDCs_MAPKAPK2 Not significant
## Unstim.cDCs_IkB Not significant
## Unstim.cDCs_NFkB Not significant
## Unstim.cDCs_ERK Not significant
## Unstim.pDCs_CREB Not significant
## Unstim.pDCs_STAT5 Not significant
## Unstim.pDCs_p38 Both
## Unstim.pDCs_STAT1 Both
## Unstim.pDCs_STAT3 Not significant
## Unstim.pDCs_S6 Not significant
## Unstim.pDCs_MAPKAPK2 Paired only
## Unstim.pDCs_IkB Not significant
## Unstim.pDCs_NFkB Both
## Unstim.pDCs_ERK Not significant
## Unstim.Th1_T_cells_CREB Both
## Unstim.Th1_T_cells_STAT5 Both
## Unstim.Th1_T_cells_p38 Not significant
## Unstim.Th1_T_cells_STAT1 Paired only
## Unstim.Th1_T_cells_STAT3 Both
## Unstim.Th1_T_cells_S6 Both
## Unstim.Th1_T_cells_MAPKAPK2 Both
## Unstim.Th1_T_cells_IkB Both
## Unstim.Th1_T_cells_NFkB Not significant
## Unstim.Th1_T_cells_ERK Both
## Unstim.Intermediate_monocytes_CREB Not significant
## Unstim.Intermediate_monocytes_STAT5 Both
## Unstim.Intermediate_monocytes_p38 Both
## Unstim.Intermediate_monocytes_STAT1 Both
## Unstim.Intermediate_monocytes_STAT3 Not significant
## Unstim.Intermediate_monocytes_S6 Not significant
## Unstim.Intermediate_monocytes_MAPKAPK2 Both
## Unstim.Intermediate_monocytes_IkB Not significant
## Unstim.Intermediate_monocytes_NFkB Not significant
## Unstim.Intermediate_monocytes_ERK Both
## Unstim.MDSCs_CREB Both
## Unstim.MDSCs_STAT5 Not significant
## Unstim.MDSCs_p38 Not significant
## Unstim.MDSCs_STAT1 Not significant
## Unstim.MDSCs_STAT3 Not significant
## Unstim.MDSCs_S6 Not significant
## Unstim.MDSCs_MAPKAPK2 Not significant
## Unstim.MDSCs_IkB Not significant
## Unstim.MDSCs_NFkB Not significant
## Unstim.MDSCs_ERK Not significant
## Unstim.Tregs_CREB Both
## Unstim.Tregs_STAT5 Both
## Unstim.Tregs_p38 Not significant
## Unstim.Tregs_STAT1 Both
## Unstim.Tregs_STAT3 Not significant
## Unstim.Tregs_S6 Both
## Unstim.Tregs_MAPKAPK2 Both
## Unstim.Tregs_IkB Not significant
## Unstim.Tregs_NFkB Both
## Unstim.Tregs_ERK Not significant
## Unstim.CD56lo_NK_cells_CREB Both
## Unstim.CD56lo_NK_cells_STAT5 Not significant
## Unstim.CD56lo_NK_cells_p38 Not significant
## Unstim.CD56lo_NK_cells_STAT1 Both
## Unstim.CD56lo_NK_cells_STAT3 Not significant
## Unstim.CD56lo_NK_cells_S6 Both
## Unstim.CD56lo_NK_cells_MAPKAPK2 Not significant
## Unstim.CD56lo_NK_cells_IkB Paired only
## Unstim.CD56lo_NK_cells_NFkB Not significant
## Unstim.CD56lo_NK_cells_ERK Not significant
## Unstim.CD56hi_NK_cells_CREB Both
## Unstim.CD56hi_NK_cells_STAT5 Not significant
## Unstim.CD56hi_NK_cells_p38 Not significant
## Unstim.CD56hi_NK_cells_STAT1 Not significant
## Unstim.CD56hi_NK_cells_STAT3 Not significant
## Unstim.CD56hi_NK_cells_S6 Both
## Unstim.CD56hi_NK_cells_MAPKAPK2 Both
## Unstim.CD56hi_NK_cells_IkB Both
## Unstim.CD56hi_NK_cells_NFkB Not significant
## Unstim.CD56hi_NK_cells_ERK Both
## Unstim.gd_T_cells_CREB Not significant
## Unstim.gd_T_cells_STAT5 Not significant
## Unstim.gd_T_cells_p38 Not significant
## Unstim.gd_T_cells_STAT1 Both
## Unstim.gd_T_cells_STAT3 Not significant
## Unstim.gd_T_cells_S6 Not significant
## Unstim.gd_T_cells_MAPKAPK2 Both
## Unstim.gd_T_cells_IkB Not significant
## Unstim.gd_T_cells_NFkB Not significant
## Unstim.gd_T_cells_ERK Not significant
## Unstim.Memory_CD4_T_cells_CREB Both
## Unstim.Memory_CD4_T_cells_STAT5 Both
## Unstim.Memory_CD4_T_cells_p38 Not significant
## Unstim.Memory_CD4_T_cells_STAT1 Both
## Unstim.Memory_CD4_T_cells_STAT3 Not significant
## Unstim.Memory_CD4_T_cells_S6 Paired only
## Unstim.Memory_CD4_T_cells_MAPKAPK2 Both
## Unstim.Memory_CD4_T_cells_IkB Paired only
## Unstim.Memory_CD4_T_cells_NFkB Paired only
## Unstim.Memory_CD4_T_cells_ERK Both
## Features
## Unstim.Granulocytes_CREB Unstim.Granulocytes_CREB
## Unstim.Granulocytes_STAT5 Unstim.Granulocytes_STAT5
## Unstim.Granulocytes_p38 Unstim.Granulocytes_p38
## Unstim.Granulocytes_STAT1 Unstim.Granulocytes_STAT1
## Unstim.Granulocytes_STAT3 Unstim.Granulocytes_STAT3
## Unstim.Granulocytes_S6 Unstim.Granulocytes_S6
## Unstim.Granulocytes_MAPKAPK2 Unstim.Granulocytes_MAPKAPK2
## Unstim.Granulocytes_IkB Unstim.Granulocytes_IkB
## Unstim.Granulocytes_NFkB Unstim.Granulocytes_NFkB
## Unstim.Granulocytes_ERK Unstim.Granulocytes_ERK
## Unstim.CD8_T_cells_CREB Unstim.CD8_T_cells_CREB
## Unstim.CD8_T_cells_STAT5 Unstim.CD8_T_cells_STAT5
## Unstim.CD8_T_cells_p38 Unstim.CD8_T_cells_p38
## Unstim.CD8_T_cells_STAT1 Unstim.CD8_T_cells_STAT1
## Unstim.CD8_T_cells_STAT3 Unstim.CD8_T_cells_STAT3
## Unstim.CD8_T_cells_S6 Unstim.CD8_T_cells_S6
## Unstim.CD8_T_cells_MAPKAPK2 Unstim.CD8_T_cells_MAPKAPK2
## Unstim.CD8_T_cells_IkB Unstim.CD8_T_cells_IkB
## Unstim.CD8_T_cells_NFkB Unstim.CD8_T_cells_NFkB
## Unstim.CD8_T_cells_ERK Unstim.CD8_T_cells_ERK
## Unstim.CD4_T_cells_CREB Unstim.CD4_T_cells_CREB
## Unstim.CD4_T_cells_STAT5 Unstim.CD4_T_cells_STAT5
## Unstim.CD4_T_cells_p38 Unstim.CD4_T_cells_p38
## Unstim.CD4_T_cells_STAT1 Unstim.CD4_T_cells_STAT1
## Unstim.CD4_T_cells_STAT3 Unstim.CD4_T_cells_STAT3
## Unstim.CD4_T_cells_S6 Unstim.CD4_T_cells_S6
## Unstim.CD4_T_cells_MAPKAPK2 Unstim.CD4_T_cells_MAPKAPK2
## Unstim.CD4_T_cells_IkB Unstim.CD4_T_cells_IkB
## Unstim.CD4_T_cells_NFkB Unstim.CD4_T_cells_NFkB
## Unstim.CD4_T_cells_ERK Unstim.CD4_T_cells_ERK
## Unstim.Naive_CD4_T_cells_CREB Unstim.Naive_CD4_T_cells_CREB
## Unstim.Naive_CD4_T_cells_STAT5 Unstim.Naive_CD4_T_cells_STAT5
## Unstim.Naive_CD4_T_cells_p38 Unstim.Naive_CD4_T_cells_p38
## Unstim.Naive_CD4_T_cells_STAT1 Unstim.Naive_CD4_T_cells_STAT1
## Unstim.Naive_CD4_T_cells_STAT3 Unstim.Naive_CD4_T_cells_STAT3
## Unstim.Naive_CD4_T_cells_S6 Unstim.Naive_CD4_T_cells_S6
## Unstim.Naive_CD4_T_cells_MAPKAPK2 Unstim.Naive_CD4_T_cells_MAPKAPK2
## Unstim.Naive_CD4_T_cells_IkB Unstim.Naive_CD4_T_cells_IkB
## Unstim.Naive_CD4_T_cells_NFkB Unstim.Naive_CD4_T_cells_NFkB
## Unstim.Naive_CD4_T_cells_ERK Unstim.Naive_CD4_T_cells_ERK
## Unstim.Naive_CD8_T_cells_CREB Unstim.Naive_CD8_T_cells_CREB
## Unstim.Naive_CD8_T_cells_STAT5 Unstim.Naive_CD8_T_cells_STAT5
## Unstim.Naive_CD8_T_cells_p38 Unstim.Naive_CD8_T_cells_p38
## Unstim.Naive_CD8_T_cells_STAT1 Unstim.Naive_CD8_T_cells_STAT1
## Unstim.Naive_CD8_T_cells_STAT3 Unstim.Naive_CD8_T_cells_STAT3
## Unstim.Naive_CD8_T_cells_S6 Unstim.Naive_CD8_T_cells_S6
## Unstim.Naive_CD8_T_cells_MAPKAPK2 Unstim.Naive_CD8_T_cells_MAPKAPK2
## Unstim.Naive_CD8_T_cells_IkB Unstim.Naive_CD8_T_cells_IkB
## Unstim.Naive_CD8_T_cells_NFkB Unstim.Naive_CD8_T_cells_NFkB
## Unstim.Naive_CD8_T_cells_ERK Unstim.Naive_CD8_T_cells_ERK
## Unstim.Memory_CD8_T_cells_CREB Unstim.Memory_CD8_T_cells_CREB
## Unstim.Memory_CD8_T_cells_STAT5 Unstim.Memory_CD8_T_cells_STAT5
## Unstim.Memory_CD8_T_cells_p38 Unstim.Memory_CD8_T_cells_p38
## Unstim.Memory_CD8_T_cells_STAT1 Unstim.Memory_CD8_T_cells_STAT1
## Unstim.Memory_CD8_T_cells_STAT3 Unstim.Memory_CD8_T_cells_STAT3
## Unstim.Memory_CD8_T_cells_S6 Unstim.Memory_CD8_T_cells_S6
## Unstim.Memory_CD8_T_cells_MAPKAPK2 Unstim.Memory_CD8_T_cells_MAPKAPK2
## Unstim.Memory_CD8_T_cells_IkB Unstim.Memory_CD8_T_cells_IkB
## Unstim.Memory_CD8_T_cells_NFkB Unstim.Memory_CD8_T_cells_NFkB
## Unstim.Memory_CD8_T_cells_ERK Unstim.Memory_CD8_T_cells_ERK
## Unstim.B_cells_CREB Unstim.B_cells_CREB
## Unstim.B_cells_STAT5 Unstim.B_cells_STAT5
## Unstim.B_cells_p38 Unstim.B_cells_p38
## Unstim.B_cells_STAT1 Unstim.B_cells_STAT1
## Unstim.B_cells_STAT3 Unstim.B_cells_STAT3
## Unstim.B_cells_S6 Unstim.B_cells_S6
## Unstim.B_cells_MAPKAPK2 Unstim.B_cells_MAPKAPK2
## Unstim.B_cells_IkB Unstim.B_cells_IkB
## Unstim.B_cells_NFkB Unstim.B_cells_NFkB
## Unstim.B_cells_ERK Unstim.B_cells_ERK
## Unstim.Classical_monocytes_CREB Unstim.Classical_monocytes_CREB
## Unstim.Classical_monocytes_STAT5 Unstim.Classical_monocytes_STAT5
## Unstim.Classical_monocytes_p38 Unstim.Classical_monocytes_p38
## Unstim.Classical_monocytes_STAT1 Unstim.Classical_monocytes_STAT1
## Unstim.Classical_monocytes_STAT3 Unstim.Classical_monocytes_STAT3
## Unstim.Classical_monocytes_S6 Unstim.Classical_monocytes_S6
## Unstim.Classical_monocytes_MAPKAPK2 Unstim.Classical_monocytes_MAPKAPK2
## Unstim.Classical_monocytes_IkB Unstim.Classical_monocytes_IkB
## Unstim.Classical_monocytes_NFkB Unstim.Classical_monocytes_NFkB
## Unstim.Classical_monocytes_ERK Unstim.Classical_monocytes_ERK
## Unstim.Nonclassical_monocytes_CREB Unstim.Nonclassical_monocytes_CREB
## Unstim.Nonclassical_monocytes_STAT5 Unstim.Nonclassical_monocytes_STAT5
## Unstim.Nonclassical_monocytes_p38 Unstim.Nonclassical_monocytes_p38
## Unstim.Nonclassical_monocytes_STAT1 Unstim.Nonclassical_monocytes_STAT1
## Unstim.Nonclassical_monocytes_STAT3 Unstim.Nonclassical_monocytes_STAT3
## Unstim.Nonclassical_monocytes_S6 Unstim.Nonclassical_monocytes_S6
## Unstim.Nonclassical_monocytes_MAPKAPK2 Unstim.Nonclassical_monocytes_MAPKAPK2
## Unstim.Nonclassical_monocytes_IkB Unstim.Nonclassical_monocytes_IkB
## Unstim.Nonclassical_monocytes_NFkB Unstim.Nonclassical_monocytes_NFkB
## Unstim.Nonclassical_monocytes_ERK Unstim.Nonclassical_monocytes_ERK
## Unstim.cDCs_CREB Unstim.cDCs_CREB
## Unstim.cDCs_STAT5 Unstim.cDCs_STAT5
## Unstim.cDCs_p38 Unstim.cDCs_p38
## Unstim.cDCs_STAT1 Unstim.cDCs_STAT1
## Unstim.cDCs_STAT3 Unstim.cDCs_STAT3
## Unstim.cDCs_S6 Unstim.cDCs_S6
## Unstim.cDCs_MAPKAPK2 Unstim.cDCs_MAPKAPK2
## Unstim.cDCs_IkB Unstim.cDCs_IkB
## Unstim.cDCs_NFkB Unstim.cDCs_NFkB
## Unstim.cDCs_ERK Unstim.cDCs_ERK
## Unstim.pDCs_CREB Unstim.pDCs_CREB
## Unstim.pDCs_STAT5 Unstim.pDCs_STAT5
## Unstim.pDCs_p38 Unstim.pDCs_p38
## Unstim.pDCs_STAT1 Unstim.pDCs_STAT1
## Unstim.pDCs_STAT3 Unstim.pDCs_STAT3
## Unstim.pDCs_S6 Unstim.pDCs_S6
## Unstim.pDCs_MAPKAPK2 Unstim.pDCs_MAPKAPK2
## Unstim.pDCs_IkB Unstim.pDCs_IkB
## Unstim.pDCs_NFkB Unstim.pDCs_NFkB
## Unstim.pDCs_ERK Unstim.pDCs_ERK
## Unstim.Th1_T_cells_CREB Unstim.Th1_T_cells_CREB
## Unstim.Th1_T_cells_STAT5 Unstim.Th1_T_cells_STAT5
## Unstim.Th1_T_cells_p38 Unstim.Th1_T_cells_p38
## Unstim.Th1_T_cells_STAT1 Unstim.Th1_T_cells_STAT1
## Unstim.Th1_T_cells_STAT3 Unstim.Th1_T_cells_STAT3
## Unstim.Th1_T_cells_S6 Unstim.Th1_T_cells_S6
## Unstim.Th1_T_cells_MAPKAPK2 Unstim.Th1_T_cells_MAPKAPK2
## Unstim.Th1_T_cells_IkB Unstim.Th1_T_cells_IkB
## Unstim.Th1_T_cells_NFkB Unstim.Th1_T_cells_NFkB
## Unstim.Th1_T_cells_ERK Unstim.Th1_T_cells_ERK
## Unstim.Intermediate_monocytes_CREB Unstim.Intermediate_monocytes_CREB
## Unstim.Intermediate_monocytes_STAT5 Unstim.Intermediate_monocytes_STAT5
## Unstim.Intermediate_monocytes_p38 Unstim.Intermediate_monocytes_p38
## Unstim.Intermediate_monocytes_STAT1 Unstim.Intermediate_monocytes_STAT1
## Unstim.Intermediate_monocytes_STAT3 Unstim.Intermediate_monocytes_STAT3
## Unstim.Intermediate_monocytes_S6 Unstim.Intermediate_monocytes_S6
## Unstim.Intermediate_monocytes_MAPKAPK2 Unstim.Intermediate_monocytes_MAPKAPK2
## Unstim.Intermediate_monocytes_IkB Unstim.Intermediate_monocytes_IkB
## Unstim.Intermediate_monocytes_NFkB Unstim.Intermediate_monocytes_NFkB
## Unstim.Intermediate_monocytes_ERK Unstim.Intermediate_monocytes_ERK
## Unstim.MDSCs_CREB Unstim.MDSCs_CREB
## Unstim.MDSCs_STAT5 Unstim.MDSCs_STAT5
## Unstim.MDSCs_p38 Unstim.MDSCs_p38
## Unstim.MDSCs_STAT1 Unstim.MDSCs_STAT1
## Unstim.MDSCs_STAT3 Unstim.MDSCs_STAT3
## Unstim.MDSCs_S6 Unstim.MDSCs_S6
## Unstim.MDSCs_MAPKAPK2 Unstim.MDSCs_MAPKAPK2
## Unstim.MDSCs_IkB Unstim.MDSCs_IkB
## Unstim.MDSCs_NFkB Unstim.MDSCs_NFkB
## Unstim.MDSCs_ERK Unstim.MDSCs_ERK
## Unstim.Tregs_CREB Unstim.Tregs_CREB
## Unstim.Tregs_STAT5 Unstim.Tregs_STAT5
## Unstim.Tregs_p38 Unstim.Tregs_p38
## Unstim.Tregs_STAT1 Unstim.Tregs_STAT1
## Unstim.Tregs_STAT3 Unstim.Tregs_STAT3
## Unstim.Tregs_S6 Unstim.Tregs_S6
## Unstim.Tregs_MAPKAPK2 Unstim.Tregs_MAPKAPK2
## Unstim.Tregs_IkB Unstim.Tregs_IkB
## Unstim.Tregs_NFkB Unstim.Tregs_NFkB
## Unstim.Tregs_ERK Unstim.Tregs_ERK
## Unstim.CD56lo_NK_cells_CREB Unstim.CD56lo_NK_cells_CREB
## Unstim.CD56lo_NK_cells_STAT5 Unstim.CD56lo_NK_cells_STAT5
## Unstim.CD56lo_NK_cells_p38 Unstim.CD56lo_NK_cells_p38
## Unstim.CD56lo_NK_cells_STAT1 Unstim.CD56lo_NK_cells_STAT1
## Unstim.CD56lo_NK_cells_STAT3 Unstim.CD56lo_NK_cells_STAT3
## Unstim.CD56lo_NK_cells_S6 Unstim.CD56lo_NK_cells_S6
## Unstim.CD56lo_NK_cells_MAPKAPK2 Unstim.CD56lo_NK_cells_MAPKAPK2
## Unstim.CD56lo_NK_cells_IkB Unstim.CD56lo_NK_cells_IkB
## Unstim.CD56lo_NK_cells_NFkB Unstim.CD56lo_NK_cells_NFkB
## Unstim.CD56lo_NK_cells_ERK Unstim.CD56lo_NK_cells_ERK
## Unstim.CD56hi_NK_cells_CREB Unstim.CD56hi_NK_cells_CREB
## Unstim.CD56hi_NK_cells_STAT5 Unstim.CD56hi_NK_cells_STAT5
## Unstim.CD56hi_NK_cells_p38 Unstim.CD56hi_NK_cells_p38
## Unstim.CD56hi_NK_cells_STAT1 Unstim.CD56hi_NK_cells_STAT1
## Unstim.CD56hi_NK_cells_STAT3 Unstim.CD56hi_NK_cells_STAT3
## Unstim.CD56hi_NK_cells_S6 Unstim.CD56hi_NK_cells_S6
## Unstim.CD56hi_NK_cells_MAPKAPK2 Unstim.CD56hi_NK_cells_MAPKAPK2
## Unstim.CD56hi_NK_cells_IkB Unstim.CD56hi_NK_cells_IkB
## Unstim.CD56hi_NK_cells_NFkB Unstim.CD56hi_NK_cells_NFkB
## Unstim.CD56hi_NK_cells_ERK Unstim.CD56hi_NK_cells_ERK
## Unstim.gd_T_cells_CREB Unstim.gd_T_cells_CREB
## Unstim.gd_T_cells_STAT5 Unstim.gd_T_cells_STAT5
## Unstim.gd_T_cells_p38 Unstim.gd_T_cells_p38
## Unstim.gd_T_cells_STAT1 Unstim.gd_T_cells_STAT1
## Unstim.gd_T_cells_STAT3 Unstim.gd_T_cells_STAT3
## Unstim.gd_T_cells_S6 Unstim.gd_T_cells_S6
## Unstim.gd_T_cells_MAPKAPK2 Unstim.gd_T_cells_MAPKAPK2
## Unstim.gd_T_cells_IkB Unstim.gd_T_cells_IkB
## Unstim.gd_T_cells_NFkB Unstim.gd_T_cells_NFkB
## Unstim.gd_T_cells_ERK Unstim.gd_T_cells_ERK
## Unstim.Memory_CD4_T_cells_CREB Unstim.Memory_CD4_T_cells_CREB
## Unstim.Memory_CD4_T_cells_STAT5 Unstim.Memory_CD4_T_cells_STAT5
## Unstim.Memory_CD4_T_cells_p38 Unstim.Memory_CD4_T_cells_p38
## Unstim.Memory_CD4_T_cells_STAT1 Unstim.Memory_CD4_T_cells_STAT1
## Unstim.Memory_CD4_T_cells_STAT3 Unstim.Memory_CD4_T_cells_STAT3
## Unstim.Memory_CD4_T_cells_S6 Unstim.Memory_CD4_T_cells_S6
## Unstim.Memory_CD4_T_cells_MAPKAPK2 Unstim.Memory_CD4_T_cells_MAPKAPK2
## Unstim.Memory_CD4_T_cells_IkB Unstim.Memory_CD4_T_cells_IkB
## Unstim.Memory_CD4_T_cells_NFkB Unstim.Memory_CD4_T_cells_NFkB
## Unstim.Memory_CD4_T_cells_ERK Unstim.Memory_CD4_T_cells_ERK
Here’s for LPS and Cocktail only:
plot_p_v_up(dfs = list("LPS" = LPS_df, "Cocktail" = Cocktail_df), sampleType = sampleType, paired_output = list("LPS" = paired_output$LPS, "Cocktail" = paired_output$Cocktail), unpaired_output = list("LPS" = unpaired_output$LPS, "Cocktail" = unpaired_output$Cocktail))
## [1] "LPS.Granulocytes_MAPKAPK2"
## [2] "LPS.Intermediate_monocytes_CREB"
## [3] "LPS.Granulocytes_NFkB"
## [4] "LPS.cDCs_ERK"
## [5] "LPS.Granulocytes_p38"
## [6] "LPS.Nonclassical_monocytes_S6"
## [7] "LPS.Th1_T_cells_IkB"
## [8] "LPS.Classical_monocytes_ERK"
## [9] "LPS.Intermediate_monocytes_S6"
## [10] "LPS.Memory_CD8_T_cells_S6"
## [11] "LPS.Granulocytes_STAT1"
## [12] "LPS.Intermediate_monocytes_ERK"
## [13] "LPS.Th1_T_cells_STAT1"
## [14] "LPS.Th1_T_cells_STAT5"
## [15] "LPS.Nonclassical_monocytes_CREB"
## [16] "LPS.cDCs_MAPKAPK2"
## [17] "LPS.Th1_T_cells_STAT3"
## [18] "LPS.Th1_T_cells_CREB"
## [19] "LPS.Classical_monocytes_MAPKAPK2"
## [20] "LPS.CD56lo_NK_cells_CREB"
## [21] "LPS.Memory_CD8_T_cells_CREB"
## [22] "LPS.B_cells_ERK"
## [23] "LPS.Th1_T_cells_ERK"
## [24] "LPS.pDCs_S6"
## [25] "LPS.pDCs_ERK"
## [26] "LPS.Memory_CD4_T_cells_p38"
## [27] "LPS.Tregs_STAT1"
## [28] "LPS.Th1_T_cells_p38"
## [29] "LPS.CD56hi_NK_cells_CREB"
## [30] "LPS.Granulocytes_CREB"
## [31] "LPS.Tregs_CREB"
## [32] "LPS.Th1_T_cells_S6"
## [33] "LPS.CD56hi_NK_cells_ERK"
## [34] "LPS.Th1_T_cells_MAPKAPK2"
## [35] "LPS.pDCs_STAT3"
## [36] "LPS.Tregs_ERK"
## [37] "LPS.Tregs_p38"
## [38] "LPS.cDCs_p38"
## [39] "LPS.B_cells_STAT5"
## [40] "LPS.cDCs_CREB"
## [41] "LPS.Naive_CD4_T_cells_ERK"
## [42] "LPS.Intermediate_monocytes_IkB"
## [43] "Cocktail.Classical_monocytes_STAT1"
## [44] "Cocktail.cDCs_STAT1"
## [45] "Cocktail.Tregs_STAT1"
## [46] "Cocktail.CD56lo_NK_cells_STAT1"
## [47] "Cocktail.Naive_CD4_T_cells_STAT1"
## [48] "Cocktail.CD4_T_cells_STAT1"
## [49] "Cocktail.CD56hi_NK_cells_STAT1"
## [50] "Cocktail.Classical_monocytes_STAT3"
## [51] "Cocktail.cDCs_STAT3"
## [52] "Cocktail.Intermediate_monocytes_STAT1"
## [53] "Cocktail.pDCs_STAT5"
## [54] "Cocktail.Memory_CD4_T_cells_STAT1"
## [55] "Cocktail.gd_T_cells_STAT1"
## [56] "Cocktail.MDSCs_STAT3"
## [57] "Cocktail.Intermediate_monocytes_CREB"
## [58] "Cocktail.pDCs_STAT1"
## [59] "Cocktail.Granulocytes_STAT1"
## [60] "Cocktail.pDCs_STAT3"
## [61] "Cocktail.Nonclassical_monocytes_STAT1"
## [62] "Cocktail.Nonclassical_monocytes_S6"
## [63] "Cocktail.Naive_CD8_T_cells_STAT1"
## [64] "Cocktail.CD56lo_NK_cells_STAT3"
## [65] "Cocktail.Memory_CD8_T_cells_CREB"
## [66] "Cocktail.Intermediate_monocytes_STAT3"
## [67] "Cocktail.Intermediate_monocytes_S6"
## [68] "Cocktail.MDSCs_STAT1"
## [69] "Cocktail.Nonclassical_monocytes_CREB"
## [70] "Cocktail.B_cells_STAT1"
## [71] "Cocktail.CD56lo_NK_cells_S6"
## [72] "Cocktail.Memory_CD8_T_cells_S6"
## [73] "Cocktail.Th1_T_cells_ERK"
## [74] "Cocktail.pDCs_ERK"
## [75] "Cocktail.CD56lo_NK_cells_CREB"
## [76] "Cocktail.Granulocytes_NFkB"
## [77] "Cocktail.CD56lo_NK_cells_ERK"
## [78] "Cocktail.Granulocytes_p38"
## [79] "Cocktail.Naive_CD8_T_cells_STAT5"
## [80] "Cocktail.Naive_CD4_T_cells_STAT5"
## [81] "Cocktail.Memory_CD8_T_cells_STAT3"
## [82] "Cocktail.CD8_T_cells_STAT5"
## [83] "Cocktail.CD8_T_cells_STAT3"
## [84] "Cocktail.CD4_T_cells_STAT5"
## [85] "Cocktail.gd_T_cells_STAT5"
## [86] "Cocktail.Memory_CD4_T_cells_STAT5"
## [87] "Cocktail.Intermediate_monocytes_MAPKAPK2"
## [88] "Cocktail.CD56hi_NK_cells_MAPKAPK2"
## [89] "Cocktail.gd_T_cells_STAT3"
## [1] "LPS.cDCs_ERK"
## [2] "LPS.Intermediate_monocytes_CREB"
## [3] "LPS.Classical_monocytes_ERK"
## [4] "LPS.Granulocytes_MAPKAPK2"
## [5] "LPS.Th1_T_cells_IkB"
## [6] "LPS.Granulocytes_NFkB"
## [7] "LPS.cDCs_MAPKAPK2"
## [8] "LPS.Th1_T_cells_STAT1"
## [9] "LPS.Th1_T_cells_STAT5"
## [10] "LPS.Classical_monocytes_MAPKAPK2"
## [11] "LPS.Nonclassical_monocytes_S6"
## [12] "LPS.Intermediate_monocytes_ERK"
## [13] "LPS.Th1_T_cells_ERK"
## [14] "LPS.B_cells_ERK"
## [15] "LPS.Granulocytes_p38"
## [16] "LPS.CD56lo_NK_cells_CREB"
## [17] "LPS.Granulocytes_STAT1"
## [18] "LPS.Intermediate_monocytes_S6"
## [19] "LPS.Th1_T_cells_STAT3"
## [20] "LPS.Th1_T_cells_CREB"
## [21] "LPS.Memory_CD8_T_cells_S6"
## [22] "LPS.Tregs_STAT1"
## [23] "LPS.pDCs_S6"
## [24] "LPS.Th1_T_cells_p38"
## [25] "LPS.Memory_CD4_T_cells_p38"
## [26] "LPS.Memory_CD8_T_cells_CREB"
## [27] "LPS.Tregs_CREB"
## [28] "LPS.Tregs_p38"
## [29] "LPS.pDCs_STAT3"
## [30] "LPS.Th1_T_cells_MAPKAPK2"
## [31] "LPS.Th1_T_cells_S6"
## [32] "LPS.B_cells_STAT5"
## [33] "LPS.CD56hi_NK_cells_ERK"
## [34] "LPS.Tregs_ERK"
## [35] "LPS.Intermediate_monocytes_STAT3"
## [36] "LPS.pDCs_ERK"
## [37] "LPS.CD56hi_NK_cells_CREB"
## [38] "LPS.Naive_CD4_T_cells_ERK"
## [39] "LPS.Memory_CD8_T_cells_p38"
## [40] "LPS.Nonclassical_monocytes_CREB"
## [41] "LPS.pDCs_CREB"
## [42] "LPS.Granulocytes_CREB"
## [43] "LPS.Naive_CD4_T_cells_IkB"
## [44] "LPS.cDCs_S6"
## [45] "LPS.Naive_CD8_T_cells_IkB"
## [46] "LPS.Memory_CD4_T_cells_STAT1"
## [47] "LPS.cDCs_CREB"
## [48] "LPS.gd_T_cells_S6"
## [49] "LPS.CD56lo_NK_cells_STAT1"
## [50] "LPS.B_cells_S6"
## [51] "Cocktail.Classical_monocytes_STAT1"
## [52] "Cocktail.cDCs_STAT1"
## [53] "Cocktail.CD56lo_NK_cells_STAT1"
## [54] "Cocktail.CD56hi_NK_cells_STAT1"
## [55] "Cocktail.Naive_CD4_T_cells_STAT1"
## [56] "Cocktail.Classical_monocytes_STAT3"
## [57] "Cocktail.Intermediate_monocytes_STAT1"
## [58] "Cocktail.Tregs_STAT1"
## [59] "Cocktail.cDCs_STAT3"
## [60] "Cocktail.CD4_T_cells_STAT1"
## [61] "Cocktail.Memory_CD8_T_cells_CREB"
## [62] "Cocktail.pDCs_STAT1"
## [63] "Cocktail.pDCs_STAT5"
## [64] "Cocktail.Intermediate_monocytes_CREB"
## [65] "Cocktail.Intermediate_monocytes_STAT3"
## [66] "Cocktail.MDSCs_STAT3"
## [67] "Cocktail.Memory_CD4_T_cells_STAT1"
## [68] "Cocktail.gd_T_cells_STAT1"
## [69] "Cocktail.pDCs_STAT3"
## [70] "Cocktail.Nonclassical_monocytes_CREB"
## [71] "Cocktail.MDSCs_STAT1"
## [72] "Cocktail.Granulocytes_STAT1"
## [73] "Cocktail.Naive_CD8_T_cells_STAT1"
## [74] "Cocktail.Nonclassical_monocytes_S6"
## [75] "Cocktail.CD56lo_NK_cells_STAT3"
## [76] "Cocktail.Memory_CD8_T_cells_S6"
## [77] "Cocktail.Th1_T_cells_ERK"
## [78] "Cocktail.Intermediate_monocytes_S6"
## [79] "Cocktail.CD56lo_NK_cells_CREB"
## [80] "Cocktail.Granulocytes_NFkB"
## [81] "Cocktail.pDCs_ERK"
## [82] "Cocktail.gd_T_cells_CREB"
## [83] "Cocktail.B_cells_STAT1"
## [84] "Cocktail.Naive_CD4_T_cells_STAT5"
## [85] "Cocktail.Naive_CD8_T_cells_STAT5"
## [86] "Cocktail.CD8_T_cells_STAT5"
## [87] "Cocktail.CD4_T_cells_STAT5"
## [88] "Cocktail.Memory_CD8_T_cells_STAT3"
## [89] "Cocktail.Memory_CD4_T_cells_STAT5"
## [90] "Cocktail.gd_T_cells_STAT5"
## [91] "Cocktail.CD56hi_NK_cells_MAPKAPK2"
## [92] "Cocktail.Intermediate_monocytes_MAPKAPK2"
## [93] "Cocktail.CD8_T_cells_STAT3"
## [1] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE
## [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [34] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [45] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [56] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [67] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [78] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
## [89] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [100] TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE
## [111] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
## [122] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [144] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE
## [199] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE
## [243] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [265] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE
## [276] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE
## [298] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [342] FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [353] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
## [364] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE
## [1] TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE
## [12] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [23] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [34] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE
## [45] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE
## [56] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE
## [67] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [78] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
## [89] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE
## [100] TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE
## [111] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
## [122] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE
## [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [144] TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE
## [155] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [166] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE
## [177] FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE
## [188] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [199] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [210] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
## [221] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [232] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE
## [243] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [254] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [265] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
## [276] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE
## [287] FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE
## [298] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [309] FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE
## [320] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
## [331] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE
## [342] FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [353] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE
## [364] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
## [375] FALSE FALSE FALSE FALSE FALSE FALSE
## unpaired_pvals paired_pvals
## LPS.Granulocytes_CREB 3.783763e-02 2.643708e-02
## LPS.Granulocytes_STAT5 1.625649e-01 9.762420e-02
## LPS.Granulocytes_p38 1.949800e-03 6.686237e-04
## LPS.Granulocytes_STAT1 1.090521e-03 7.387796e-04
## LPS.Granulocytes_STAT3 6.254134e-02 6.730100e-02
## LPS.Granulocytes_S6 4.989709e-01 3.994294e-01
## LPS.Granulocytes_MAPKAPK2 1.802462e-04 1.857843e-04
## LPS.Granulocytes_IkB 2.455289e-01 1.540945e-01
## LPS.Granulocytes_NFkB 4.832534e-05 1.262582e-04
## LPS.Granulocytes_ERK 1.906192e-01 1.422160e-01
## LPS.CD8_T_cells_CREB 8.995880e-02 4.850847e-02
## LPS.CD8_T_cells_STAT5 1.121871e-01 1.658291e-01
## LPS.CD8_T_cells_p38 5.523849e-03 1.481440e-02
## LPS.CD8_T_cells_STAT1 9.345168e-02 1.218269e-01
## LPS.CD8_T_cells_STAT3 2.363703e-01 3.094741e-01
## LPS.CD8_T_cells_S6 4.218953e-03 1.010782e-02
## LPS.CD8_T_cells_MAPKAPK2 1.312338e-01 2.100037e-01
## LPS.CD8_T_cells_IkB 4.404673e-02 9.638713e-02
## LPS.CD8_T_cells_NFkB 8.720223e-02 1.382374e-01
## LPS.CD8_T_cells_ERK 4.637117e-02 7.781786e-02
## LPS.CD4_T_cells_CREB 3.784971e-02 5.177601e-02
## LPS.CD4_T_cells_STAT5 3.008470e-01 3.841470e-01
## LPS.CD4_T_cells_p38 1.875365e-03 7.278507e-03
## LPS.CD4_T_cells_STAT1 3.325704e-03 1.111920e-02
## LPS.CD4_T_cells_STAT3 7.468565e-01 7.555742e-01
## LPS.CD4_T_cells_S6 1.563098e-02 4.702247e-02
## LPS.CD4_T_cells_MAPKAPK2 2.256486e-01 3.192959e-01
## LPS.CD4_T_cells_IkB 6.039628e-03 2.576573e-02
## LPS.CD4_T_cells_NFkB 8.750321e-02 1.327405e-01
## LPS.CD4_T_cells_ERK 2.184896e-02 4.150028e-02
## LPS.Naive_CD4_T_cells_CREB 1.664633e-01 2.022860e-01
## LPS.Naive_CD4_T_cells_STAT5 8.856334e-02 1.313583e-01
## LPS.Naive_CD4_T_cells_p38 1.750436e-02 5.074675e-02
## LPS.Naive_CD4_T_cells_STAT1 3.706196e-03 8.058377e-03
## LPS.Naive_CD4_T_cells_STAT3 2.720142e-01 3.041328e-01
## LPS.Naive_CD4_T_cells_S6 3.817540e-02 9.200947e-02
## LPS.Naive_CD4_T_cells_MAPKAPK2 3.811198e-01 4.829166e-01
## LPS.Naive_CD4_T_cells_IkB 2.263725e-03 1.369260e-02
## LPS.Naive_CD4_T_cells_NFkB 2.432129e-01 3.262682e-01
## LPS.Naive_CD4_T_cells_ERK 5.947531e-03 1.250720e-02
## LPS.Naive_CD8_T_cells_CREB 6.085781e-01 6.159240e-01
## LPS.Naive_CD8_T_cells_STAT5 2.006932e-02 4.825051e-02
## LPS.Naive_CD8_T_cells_p38 2.552659e-02 5.201532e-02
## LPS.Naive_CD8_T_cells_STAT1 4.533740e-02 6.180609e-02
## LPS.Naive_CD8_T_cells_STAT3 4.434606e-02 9.929234e-02
## LPS.Naive_CD8_T_cells_S6 8.434542e-02 1.865535e-01
## LPS.Naive_CD8_T_cells_MAPKAPK2 2.819456e-01 4.052953e-01
## LPS.Naive_CD8_T_cells_IkB 3.193868e-03 1.374692e-02
## LPS.Naive_CD8_T_cells_NFkB 1.912033e-01 2.662679e-01
## LPS.Naive_CD8_T_cells_ERK 1.923678e-02 4.268931e-02
## LPS.Memory_CD8_T_cells_CREB 1.002414e-03 3.572267e-04
## LPS.Memory_CD8_T_cells_STAT5 1.496193e-01 1.598064e-01
## LPS.Memory_CD8_T_cells_p38 8.087042e-04 5.756421e-03
## LPS.Memory_CD8_T_cells_STAT1 4.768323e-02 9.429568e-02
## LPS.Memory_CD8_T_cells_STAT3 4.125815e-01 5.023914e-01
## LPS.Memory_CD8_T_cells_S6 1.427250e-04 2.013783e-05
## LPS.Memory_CD8_T_cells_MAPKAPK2 1.394502e-01 1.703192e-01
## LPS.Memory_CD8_T_cells_IkB 9.722163e-02 1.916266e-01
## LPS.Memory_CD8_T_cells_NFkB 1.158359e-01 1.678764e-01
## LPS.Memory_CD8_T_cells_ERK 9.189339e-02 1.137438e-01
## LPS.B_cells_CREB 1.688791e-01 1.340869e-01
## LPS.B_cells_STAT5 2.638342e-04 3.810488e-03
## LPS.B_cells_p38 1.784604e-01 1.577801e-01
## LPS.B_cells_STAT1 2.210770e-02 2.818577e-02
## LPS.B_cells_STAT3 1.145218e-03 3.969543e-03
## LPS.B_cells_S6 1.018298e-02 1.854926e-02
## LPS.B_cells_MAPKAPK2 9.023285e-01 9.188352e-01
## LPS.B_cells_IkB 7.304628e-01 7.153502e-01
## LPS.B_cells_NFkB 9.405601e-01 9.362869e-01
## LPS.B_cells_ERK 3.164204e-04 2.349311e-03
## LPS.Classical_monocytes_CREB 7.697039e-02 7.355686e-02
## LPS.Classical_monocytes_STAT5 4.168298e-01 4.604080e-01
## LPS.Classical_monocytes_p38 6.567651e-02 5.213851e-02
## LPS.Classical_monocytes_STAT1 3.393272e-01 3.237891e-01
## LPS.Classical_monocytes_STAT3 3.633153e-01 3.528241e-01
## LPS.Classical_monocytes_S6 5.295564e-02 6.889808e-02
## LPS.Classical_monocytes_MAPKAPK2 3.442018e-04 4.257396e-03
## LPS.Classical_monocytes_IkB 5.301733e-01 4.299975e-01
## LPS.Classical_monocytes_NFkB 8.241754e-02 5.096554e-02
## LPS.Classical_monocytes_ERK 2.980821e-05 5.865644e-04
## LPS.Nonclassical_monocytes_CREB 3.721711e-02 4.308902e-03
## LPS.Nonclassical_monocytes_STAT5 9.098006e-01 9.061150e-01
## LPS.Nonclassical_monocytes_p38 3.985547e-01 1.140778e-01
## LPS.Nonclassical_monocytes_STAT1 5.819131e-01 4.504055e-01
## LPS.Nonclassical_monocytes_STAT3 2.098742e-01 2.241985e-01
## LPS.Nonclassical_monocytes_S6 1.508872e-03 8.007305e-04
## LPS.Nonclassical_monocytes_MAPKAPK2 9.518378e-01 9.392337e-01
## LPS.Nonclassical_monocytes_IkB 2.018135e-01 4.718950e-03
## LPS.Nonclassical_monocytes_NFkB 5.591591e-01 5.041067e-01
## LPS.Nonclassical_monocytes_ERK 5.248101e-01 4.548691e-01
## LPS.cDCs_CREB 4.463392e-02 4.330073e-02
## LPS.cDCs_STAT5 3.475004e-01 3.752976e-01
## LPS.cDCs_p38 5.102548e-02 4.372824e-02
## LPS.cDCs_STAT1 3.750960e-01 3.765760e-01
## LPS.cDCs_STAT3 2.200325e-01 1.894526e-01
## LPS.cDCs_S6 4.111547e-02 5.462969e-02
## LPS.cDCs_MAPKAPK2 1.520158e-04 3.370337e-03
## LPS.cDCs_IkB 8.088105e-01 7.414717e-01
## LPS.cDCs_NFkB 8.281548e-02 4.839562e-02
## LPS.cDCs_ERK 6.900363e-06 2.456489e-04
## LPS.pDCs_CREB 4.790057e-02 7.502808e-02
## LPS.pDCs_STAT5 2.195491e-01 7.898268e-02
## LPS.pDCs_p38 1.192723e-01 1.264610e-01
## LPS.pDCs_STAT1 8.424139e-02 6.498668e-02
## LPS.pDCs_STAT3 7.655393e-03 2.013856e-02
## LPS.pDCs_S6 1.287328e-02 8.605304e-03
## LPS.pDCs_MAPKAPK2 1.628653e-01 1.295491e-01
## LPS.pDCs_IkB 4.295403e-01 4.827252e-01
## LPS.pDCs_NFkB 5.443848e-01 5.302885e-01
## LPS.pDCs_ERK 3.259542e-02 1.167659e-02
## LPS.Th1_T_cells_CREB 1.072605e-03 1.180558e-03
## LPS.Th1_T_cells_STAT5 1.627107e-04 1.250588e-03
## LPS.Th1_T_cells_p38 5.247840e-04 4.526139e-03
## LPS.Th1_T_cells_STAT1 1.522706e-04 3.481618e-04
## LPS.Th1_T_cells_STAT3 3.383236e-04 4.152809e-04
## LPS.Th1_T_cells_S6 1.057288e-02 2.022629e-02
## LPS.Th1_T_cells_MAPKAPK2 4.409969e-03 1.289875e-02
## LPS.Th1_T_cells_IkB 1.552394e-04 2.727190e-04
## LPS.Th1_T_cells_NFkB 1.294246e-01 2.038822e-01
## LPS.Th1_T_cells_ERK 5.697479e-04 4.099494e-03
## LPS.Intermediate_monocytes_CREB 2.486140e-04 4.002258e-04
## LPS.Intermediate_monocytes_STAT5 3.005911e-01 2.657163e-01
## LPS.Intermediate_monocytes_p38 6.780650e-01 5.091597e-01
## LPS.Intermediate_monocytes_STAT1 4.634725e-03 5.016941e-03
## LPS.Intermediate_monocytes_STAT3 1.222113e-02 2.953397e-02
## LPS.Intermediate_monocytes_S6 2.524553e-03 1.032253e-03
## LPS.Intermediate_monocytes_MAPKAPK2 4.596377e-01 4.907907e-01
## LPS.Intermediate_monocytes_IkB 8.448468e-02 3.552542e-02
## LPS.Intermediate_monocytes_NFkB 5.854665e-02 4.172859e-02
## LPS.Intermediate_monocytes_ERK 8.155799e-04 1.414061e-03
## LPS.MDSCs_CREB 4.439090e-01 3.859424e-01
## LPS.MDSCs_STAT5 7.505726e-01 7.589233e-01
## LPS.MDSCs_p38 5.064226e-01 4.147920e-01
## LPS.MDSCs_STAT1 8.179251e-01 7.919136e-01
## LPS.MDSCs_STAT3 1.021537e-01 2.109153e-01
## LPS.MDSCs_S6 3.776016e-01 3.686788e-01
## LPS.MDSCs_MAPKAPK2 8.929331e-01 8.789827e-01
## LPS.MDSCs_IkB 4.683011e-01 3.429283e-01
## LPS.MDSCs_NFkB 6.688987e-01 5.848676e-01
## LPS.MDSCs_ERK 6.659650e-01 5.945577e-01
## LPS.Tregs_CREB 1.111851e-03 7.053751e-03
## LPS.Tregs_STAT5 6.884383e-02 9.076124e-03
## LPS.Tregs_p38 2.245698e-03 1.090497e-02
## LPS.Tregs_STAT1 4.891992e-04 3.608167e-03
## LPS.Tregs_STAT3 9.408616e-01 9.443341e-01
## LPS.Tregs_S6 1.750596e-01 2.536198e-01
## LPS.Tregs_MAPKAPK2 4.159939e-01 4.838047e-01
## LPS.Tregs_IkB 1.723351e-01 2.528793e-01
## LPS.Tregs_NFkB 4.308424e-01 5.076842e-01
## LPS.Tregs_ERK 1.152097e-02 1.708144e-02
## LPS.CD56lo_NK_cells_CREB 5.013129e-05 5.502187e-04
## LPS.CD56lo_NK_cells_STAT5 5.116511e-01 5.529819e-01
## LPS.CD56lo_NK_cells_p38 3.415222e-01 4.095811e-01
## LPS.CD56lo_NK_cells_STAT1 3.112305e-03 2.360121e-02
## LPS.CD56lo_NK_cells_STAT3 3.063608e-01 4.254197e-01
## LPS.CD56lo_NK_cells_S6 1.117189e-01 1.482539e-01
## LPS.CD56lo_NK_cells_MAPKAPK2 2.181960e-01 3.319048e-01
## LPS.CD56lo_NK_cells_IkB 6.356498e-01 6.856536e-01
## LPS.CD56lo_NK_cells_NFkB 4.049508e-01 4.359202e-01
## LPS.CD56lo_NK_cells_ERK 1.201455e-01 1.846198e-01
## LPS.CD56hi_NK_cells_CREB 9.768998e-03 4.914787e-03
## LPS.CD56hi_NK_cells_STAT5 9.249209e-01 9.084947e-01
## LPS.CD56hi_NK_cells_p38 3.906871e-01 4.159952e-01
## LPS.CD56hi_NK_cells_STAT1 3.246819e-01 3.197096e-01
## LPS.CD56hi_NK_cells_STAT3 3.646850e-01 3.103363e-01
## LPS.CD56hi_NK_cells_S6 3.229003e-02 1.262770e-02
## LPS.CD56hi_NK_cells_MAPKAPK2 1.949345e-02 3.306435e-03
## LPS.CD56hi_NK_cells_IkB 6.552864e-01 6.317264e-01
## LPS.CD56hi_NK_cells_NFkB 2.391147e-01 2.489655e-01
## LPS.CD56hi_NK_cells_ERK 6.713890e-03 1.308747e-02
## LPS.gd_T_cells_CREB 6.889516e-02 5.211790e-02
## LPS.gd_T_cells_STAT5 5.747189e-01 6.137692e-01
## LPS.gd_T_cells_p38 9.157938e-03 2.894868e-02
## LPS.gd_T_cells_STAT1 2.170140e-02 2.874559e-02
## LPS.gd_T_cells_STAT3 3.906916e-01 2.886266e-01
## LPS.gd_T_cells_S6 1.610006e-02 2.294261e-02
## LPS.gd_T_cells_MAPKAPK2 1.703086e-01 2.400310e-01
## LPS.gd_T_cells_IkB 2.180042e-01 2.794451e-01
## LPS.gd_T_cells_NFkB 2.407166e-01 2.820138e-01
## LPS.gd_T_cells_ERK 7.423228e-02 1.583610e-01
## LPS.Memory_CD4_T_cells_CREB 5.949051e-03 7.466765e-03
## LPS.Memory_CD4_T_cells_STAT5 6.114509e-01 6.636549e-01
## LPS.Memory_CD4_T_cells_p38 1.696984e-04 9.710320e-04
## LPS.Memory_CD4_T_cells_STAT1 1.587635e-03 9.920857e-03
## LPS.Memory_CD4_T_cells_STAT3 7.188818e-01 7.397369e-01
## LPS.Memory_CD4_T_cells_S6 5.404505e-02 8.560727e-02
## LPS.Memory_CD4_T_cells_MAPKAPK2 1.361428e-01 2.102232e-01
## LPS.Memory_CD4_T_cells_IkB 3.582133e-02 6.368846e-02
## LPS.Memory_CD4_T_cells_NFkB 8.118870e-02 1.096778e-01
## LPS.Memory_CD4_T_cells_ERK 2.943559e-02 5.272070e-02
## Cocktail.Granulocytes_CREB 1.372723e-01 7.654011e-02
## Cocktail.Granulocytes_STAT5 6.036978e-02 7.086786e-02
## Cocktail.Granulocytes_p38 3.969318e-02 1.087332e-02
## Cocktail.Granulocytes_STAT1 3.729284e-03 1.390396e-03
## Cocktail.Granulocytes_STAT3 7.332063e-01 7.430882e-01
## Cocktail.Granulocytes_S6 8.244039e-01 7.600163e-01
## Cocktail.Granulocytes_MAPKAPK2 6.410404e-01 6.039015e-01
## Cocktail.Granulocytes_IkB 2.413524e-01 3.098739e-01
## Cocktail.Granulocytes_NFkB 8.494146e-03 1.298083e-02
## Cocktail.Granulocytes_ERK 1.591356e-01 9.849303e-02
## Cocktail.CD8_T_cells_CREB 1.105485e-02 4.894132e-02
## Cocktail.CD8_T_cells_STAT5 7.405472e-05 1.382645e-04
## Cocktail.CD8_T_cells_p38 2.610063e-01 8.181273e-02
## Cocktail.CD8_T_cells_STAT1 1.957775e-01 1.296004e-01
## Cocktail.CD8_T_cells_STAT3 4.144848e-03 2.078093e-04
## Cocktail.CD8_T_cells_S6 2.583585e-03 7.600890e-03
## Cocktail.CD8_T_cells_MAPKAPK2 1.324119e-01 2.030600e-01
## Cocktail.CD8_T_cells_IkB 7.935428e-01 7.705339e-01
## Cocktail.CD8_T_cells_NFkB 3.213584e-01 2.971104e-01
## Cocktail.CD8_T_cells_ERK 7.487132e-02 7.435372e-02
## Cocktail.CD4_T_cells_CREB 7.619189e-01 8.016618e-01
## Cocktail.CD4_T_cells_STAT5 6.778096e-05 6.181327e-04
## Cocktail.CD4_T_cells_p38 9.860246e-01 9.573985e-01
## Cocktail.CD4_T_cells_STAT1 3.912789e-05 1.411548e-05
## Cocktail.CD4_T_cells_STAT3 2.856236e-01 2.282371e-01
## Cocktail.CD4_T_cells_S6 2.146608e-03 1.736947e-03
## Cocktail.CD4_T_cells_MAPKAPK2 1.190015e-02 3.450640e-02
## Cocktail.CD4_T_cells_IkB 7.981989e-01 7.797428e-01
## Cocktail.CD4_T_cells_NFkB 2.197953e-02 1.854070e-02
## Cocktail.CD4_T_cells_ERK 6.194067e-01 6.048827e-01
## Cocktail.Naive_CD4_T_cells_CREB 3.560716e-01 3.747882e-01
## Cocktail.Naive_CD4_T_cells_STAT5 9.217475e-07 3.690274e-05
## Cocktail.Naive_CD4_T_cells_p38 3.550968e-01 1.144599e-02
## Cocktail.Naive_CD4_T_cells_STAT1 1.387196e-05 1.055501e-05
## Cocktail.Naive_CD4_T_cells_STAT3 3.611570e-01 2.923945e-01
## Cocktail.Naive_CD4_T_cells_S6 3.018856e-02 1.979025e-02
## Cocktail.Naive_CD4_T_cells_MAPKAPK2 1.685303e-02 4.886949e-02
## Cocktail.Naive_CD4_T_cells_IkB 5.198827e-01 5.086278e-01
## Cocktail.Naive_CD4_T_cells_NFkB 9.153930e-03 1.503021e-02
## Cocktail.Naive_CD4_T_cells_ERK 5.523448e-01 5.549189e-01
## Cocktail.Naive_CD8_T_cells_CREB 6.827006e-01 7.561352e-01
## Cocktail.Naive_CD8_T_cells_STAT5 1.506443e-06 1.590328e-05
## Cocktail.Naive_CD8_T_cells_p38 2.454057e-01 3.577070e-02
## Cocktail.Naive_CD8_T_cells_STAT1 4.841112e-03 2.232547e-03
## Cocktail.Naive_CD8_T_cells_STAT3 1.353675e-01 1.016751e-02
## Cocktail.Naive_CD8_T_cells_S6 5.829137e-02 5.949012e-02
## Cocktail.Naive_CD8_T_cells_MAPKAPK2 5.192037e-02 1.118558e-01
## Cocktail.Naive_CD8_T_cells_IkB 4.120198e-01 3.820106e-01
## Cocktail.Naive_CD8_T_cells_NFkB 2.664262e-02 5.505388e-02
## Cocktail.Naive_CD8_T_cells_ERK 1.424804e-01 1.540346e-01
## Cocktail.Memory_CD8_T_cells_CREB 3.788877e-04 8.280178e-04
## Cocktail.Memory_CD8_T_cells_STAT5 1.652558e-02 1.919699e-02
## Cocktail.Memory_CD8_T_cells_p38 8.370742e-01 7.995565e-01
## Cocktail.Memory_CD8_T_cells_STAT1 4.291684e-01 3.189040e-01
## Cocktail.Memory_CD8_T_cells_STAT3 1.725063e-04 1.535046e-04
## Cocktail.Memory_CD8_T_cells_S6 2.328950e-04 2.050139e-03
## Cocktail.Memory_CD8_T_cells_MAPKAPK2 8.034781e-01 8.207947e-01
## Cocktail.Memory_CD8_T_cells_IkB 6.777275e-01 6.450120e-01
## Cocktail.Memory_CD8_T_cells_NFkB 5.919293e-03 2.342677e-02
## Cocktail.Memory_CD8_T_cells_ERK 4.384657e-03 1.068121e-02
## Cocktail.B_cells_CREB 4.937880e-03 1.299845e-02
## Cocktail.B_cells_STAT5 2.288309e-02 6.888140e-03
## Cocktail.B_cells_p38 1.693435e-02 5.075257e-03
## Cocktail.B_cells_STAT1 3.303124e-02 1.447228e-02
## Cocktail.B_cells_STAT3 7.760841e-01 6.675445e-01
## Cocktail.B_cells_S6 2.850547e-02 4.220920e-02
## Cocktail.B_cells_MAPKAPK2 9.417264e-01 9.548476e-01
## Cocktail.B_cells_IkB 9.206397e-01 9.230658e-01
## Cocktail.B_cells_NFkB 3.614471e-01 3.758984e-01
## Cocktail.B_cells_ERK 1.668044e-02 4.291246e-02
## Cocktail.Classical_monocytes_CREB 1.939082e-01 1.558125e-01
## Cocktail.Classical_monocytes_STAT5 9.342864e-01 8.922295e-01
## Cocktail.Classical_monocytes_p38 1.094087e-01 3.463008e-02
## Cocktail.Classical_monocytes_STAT1 2.841755e-08 7.789758e-07
## Cocktail.Classical_monocytes_STAT3 6.855633e-06 1.565196e-05
## Cocktail.Classical_monocytes_S6 1.246413e-01 1.264242e-01
## Cocktail.Classical_monocytes_MAPKAPK2 2.842675e-01 2.877560e-01
## Cocktail.Classical_monocytes_IkB 5.950901e-01 4.427354e-01
## Cocktail.Classical_monocytes_NFkB 4.523743e-01 3.357986e-01
## Cocktail.Classical_monocytes_ERK 5.187035e-01 4.689330e-01
## Cocktail.Nonclassical_monocytes_CREB 3.876510e-03 8.650712e-03
## Cocktail.Nonclassical_monocytes_STAT5 4.378046e-01 1.930798e-01
## Cocktail.Nonclassical_monocytes_p38 2.036744e-01 1.467368e-01
## Cocktail.Nonclassical_monocytes_STAT1 6.214642e-02 2.287062e-03
## Cocktail.Nonclassical_monocytes_STAT3 4.212228e-01 3.111970e-01
## Cocktail.Nonclassical_monocytes_S6 4.689136e-03 1.563354e-03
## Cocktail.Nonclassical_monocytes_MAPKAPK2 5.149079e-02 2.379052e-02
## Cocktail.Nonclassical_monocytes_IkB 6.351573e-02 9.667225e-02
## Cocktail.Nonclassical_monocytes_NFkB 7.876686e-01 8.073924e-01
## Cocktail.Nonclassical_monocytes_ERK 1.744932e-01 1.139294e-01
## Cocktail.cDCs_CREB 1.263203e-01 9.709402e-02
## Cocktail.cDCs_STAT5 7.647796e-01 6.162087e-01
## Cocktail.cDCs_p38 1.282695e-01 4.313086e-02
## Cocktail.cDCs_STAT1 5.664502e-08 8.851559e-07
## Cocktail.cDCs_STAT3 1.307988e-05 1.848289e-05
## Cocktail.cDCs_S6 1.067419e-01 1.070221e-01
## Cocktail.cDCs_MAPKAPK2 2.207743e-01 2.359625e-01
## Cocktail.cDCs_IkB 7.626307e-01 6.272978e-01
## Cocktail.cDCs_NFkB 3.851362e-01 2.563916e-01
## Cocktail.cDCs_ERK 6.458639e-01 6.060402e-01
## Cocktail.pDCs_CREB 1.603890e-01 2.980323e-02
## Cocktail.pDCs_STAT5 6.491161e-04 2.011305e-04
## Cocktail.pDCs_p38 4.607230e-02 3.198227e-02
## Cocktail.pDCs_STAT1 7.492047e-04 1.716831e-03
## Cocktail.pDCs_STAT3 3.302022e-03 1.456874e-03
## Cocktail.pDCs_S6 7.388744e-01 6.015124e-01
## Cocktail.pDCs_MAPKAPK2 3.158995e-01 2.974472e-01
## Cocktail.pDCs_IkB 6.574854e-01 6.514537e-01
## Cocktail.pDCs_NFkB 6.359373e-01 5.050466e-01
## Cocktail.pDCs_ERK 1.171944e-02 1.017372e-02
## Cocktail.Th1_T_cells_CREB 5.680841e-01 5.316317e-01
## Cocktail.Th1_T_cells_STAT5 2.787419e-02 2.875396e-02
## Cocktail.Th1_T_cells_p38 9.392599e-02 6.677759e-02
## Cocktail.Th1_T_cells_STAT1 3.925863e-01 3.639653e-01
## Cocktail.Th1_T_cells_STAT3 4.461670e-02 4.337438e-02
## Cocktail.Th1_T_cells_S6 2.304310e-01 2.303534e-01
## Cocktail.Th1_T_cells_MAPKAPK2 1.196136e-01 1.665136e-01
## Cocktail.Th1_T_cells_IkB 4.121526e-02 5.902332e-02
## Cocktail.Th1_T_cells_NFkB 5.955223e-01 5.593781e-01
## Cocktail.Th1_T_cells_ERK 1.307151e-03 5.133213e-03
## Cocktail.Intermediate_monocytes_CREB 1.127104e-03 1.116942e-03
## Cocktail.Intermediate_monocytes_STAT5 4.433319e-01 3.608981e-01
## Cocktail.Intermediate_monocytes_p38 6.886138e-01 6.699712e-01
## Cocktail.Intermediate_monocytes_STAT1 3.336481e-05 6.527878e-05
## Cocktail.Intermediate_monocytes_STAT3 2.230762e-03 2.962565e-03
## Cocktail.Intermediate_monocytes_S6 1.042892e-02 3.125920e-03
## Cocktail.Intermediate_monocytes_MAPKAPK2 2.393513e-03 1.320800e-03
## Cocktail.Intermediate_monocytes_IkB 4.146176e-01 2.146026e-01
## Cocktail.Intermediate_monocytes_NFkB 5.150615e-01 4.151476e-01
## Cocktail.Intermediate_monocytes_ERK 5.451841e-01 4.992171e-01
## Cocktail.MDSCs_CREB 2.312746e-01 2.156919e-01
## Cocktail.MDSCs_STAT5 5.408239e-01 5.439189e-01
## Cocktail.MDSCs_p38 3.518591e-01 2.211300e-01
## Cocktail.MDSCs_STAT1 9.750655e-03 6.265596e-03
## Cocktail.MDSCs_STAT3 2.901321e-03 9.500139e-04
## Cocktail.MDSCs_S6 2.378545e-01 2.516392e-01
## Cocktail.MDSCs_MAPKAPK2 3.387969e-01 3.139538e-01
## Cocktail.MDSCs_IkB 5.414387e-02 8.515345e-02
## Cocktail.MDSCs_NFkB 6.702804e-01 6.050355e-01
## Cocktail.MDSCs_ERK 3.005668e-01 3.186393e-01
## Cocktail.Tregs_CREB 4.747852e-01 4.855306e-01
## Cocktail.Tregs_STAT5 4.776483e-02 5.753623e-02
## Cocktail.Tregs_p38 4.895483e-01 8.439426e-02
## Cocktail.Tregs_STAT1 3.442452e-05 4.924785e-06
## Cocktail.Tregs_STAT3 3.484357e-01 2.346570e-01
## Cocktail.Tregs_S6 4.160392e-01 3.081049e-01
## Cocktail.Tregs_MAPKAPK2 2.261250e-02 3.508891e-02
## Cocktail.Tregs_IkB 7.806999e-01 8.237691e-01
## Cocktail.Tregs_NFkB 1.167344e-01 1.068907e-01
## Cocktail.Tregs_ERK 7.439415e-02 8.855175e-02
## Cocktail.CD56lo_NK_cells_CREB 8.455179e-03 1.494249e-02
## Cocktail.CD56lo_NK_cells_STAT5 3.063707e-01 2.485959e-01
## Cocktail.CD56lo_NK_cells_p38 2.620391e-02 1.703064e-02
## Cocktail.CD56lo_NK_cells_STAT1 2.076970e-06 1.029504e-05
## Cocktail.CD56lo_NK_cells_STAT3 4.151752e-03 1.171908e-03
## Cocktail.CD56lo_NK_cells_S6 1.339833e-02 2.573930e-03
## Cocktail.CD56lo_NK_cells_MAPKAPK2 1.053266e-01 9.598332e-02
## Cocktail.CD56lo_NK_cells_IkB 8.743075e-01 8.746084e-01
## Cocktail.CD56lo_NK_cells_NFkB 4.140349e-02 7.344984e-02
## Cocktail.CD56lo_NK_cells_ERK 8.315580e-03 6.847928e-03
## Cocktail.CD56hi_NK_cells_CREB 5.888640e-01 6.111748e-01
## Cocktail.CD56hi_NK_cells_STAT5 6.212979e-02 6.115063e-02
## Cocktail.CD56hi_NK_cells_p38 1.550163e-01 1.215461e-01
## Cocktail.CD56hi_NK_cells_STAT1 3.337674e-06 2.983835e-05
## Cocktail.CD56hi_NK_cells_STAT3 1.055475e-01 7.141878e-02
## Cocktail.CD56hi_NK_cells_S6 9.356835e-01 9.286171e-01
## Cocktail.CD56hi_NK_cells_MAPKAPK2 2.028708e-05 1.203565e-04
## Cocktail.CD56hi_NK_cells_IkB 6.147455e-01 5.801014e-01
## Cocktail.CD56hi_NK_cells_NFkB 8.730336e-01 8.761052e-01
## Cocktail.CD56hi_NK_cells_ERK 3.710699e-01 2.603457e-01
## Cocktail.gd_T_cells_CREB 1.109352e-02 3.715116e-02
## Cocktail.gd_T_cells_STAT5 5.808676e-04 8.337238e-04
## Cocktail.gd_T_cells_p38 3.567935e-01 3.415657e-01
## Cocktail.gd_T_cells_STAT1 5.858359e-03 1.132979e-03
## Cocktail.gd_T_cells_STAT3 1.942003e-02 2.531648e-03
## Cocktail.gd_T_cells_S6 8.956167e-03 3.901922e-02
## Cocktail.gd_T_cells_MAPKAPK2 4.219607e-01 4.677677e-01
## Cocktail.gd_T_cells_IkB 8.630195e-01 8.739116e-01
## Cocktail.gd_T_cells_NFkB 1.359771e-01 1.610754e-01
## Cocktail.gd_T_cells_ERK 1.907227e-02 4.130626e-02
## Cocktail.Memory_CD4_T_cells_CREB 3.344587e-01 4.220362e-01
## Cocktail.Memory_CD4_T_cells_STAT5 1.739381e-04 1.217589e-03
## Cocktail.Memory_CD4_T_cells_p38 9.918864e-01 9.814792e-01
## Cocktail.Memory_CD4_T_cells_STAT1 3.296811e-03 3.919114e-04
## Cocktail.Memory_CD4_T_cells_STAT3 6.549891e-01 6.106366e-01
## Cocktail.Memory_CD4_T_cells_S6 8.373510e-03 3.548889e-03
## Cocktail.Memory_CD4_T_cells_MAPKAPK2 1.485663e-02 4.008193e-02
## Cocktail.Memory_CD4_T_cells_IkB 8.382569e-01 8.207364e-01
## Cocktail.Memory_CD4_T_cells_NFkB 1.989691e-02 1.709443e-02
## Cocktail.Memory_CD4_T_cells_ERK 4.191026e-01 4.036851e-01
## Significance_Bonferroni
## LPS.Granulocytes_CREB Not significant
## LPS.Granulocytes_STAT5 Not significant
## LPS.Granulocytes_p38 Not significant
## LPS.Granulocytes_STAT1 Not significant
## LPS.Granulocytes_STAT3 Not significant
## LPS.Granulocytes_S6 Not significant
## LPS.Granulocytes_MAPKAPK2 Not significant
## LPS.Granulocytes_IkB Not significant
## LPS.Granulocytes_NFkB Both
## LPS.Granulocytes_ERK Not significant
## LPS.CD8_T_cells_CREB Not significant
## LPS.CD8_T_cells_STAT5 Not significant
## LPS.CD8_T_cells_p38 Not significant
## LPS.CD8_T_cells_STAT1 Not significant
## LPS.CD8_T_cells_STAT3 Not significant
## LPS.CD8_T_cells_S6 Not significant
## LPS.CD8_T_cells_MAPKAPK2 Not significant
## LPS.CD8_T_cells_IkB Not significant
## LPS.CD8_T_cells_NFkB Not significant
## LPS.CD8_T_cells_ERK Not significant
## LPS.CD4_T_cells_CREB Not significant
## LPS.CD4_T_cells_STAT5 Not significant
## LPS.CD4_T_cells_p38 Not significant
## LPS.CD4_T_cells_STAT1 Not significant
## LPS.CD4_T_cells_STAT3 Not significant
## LPS.CD4_T_cells_S6 Not significant
## LPS.CD4_T_cells_MAPKAPK2 Not significant
## LPS.CD4_T_cells_IkB Not significant
## LPS.CD4_T_cells_NFkB Not significant
## LPS.CD4_T_cells_ERK Not significant
## LPS.Naive_CD4_T_cells_CREB Not significant
## LPS.Naive_CD4_T_cells_STAT5 Not significant
## LPS.Naive_CD4_T_cells_p38 Not significant
## LPS.Naive_CD4_T_cells_STAT1 Not significant
## LPS.Naive_CD4_T_cells_STAT3 Not significant
## LPS.Naive_CD4_T_cells_S6 Not significant
## LPS.Naive_CD4_T_cells_MAPKAPK2 Not significant
## LPS.Naive_CD4_T_cells_IkB Not significant
## LPS.Naive_CD4_T_cells_NFkB Not significant
## LPS.Naive_CD4_T_cells_ERK Not significant
## LPS.Naive_CD8_T_cells_CREB Not significant
## LPS.Naive_CD8_T_cells_STAT5 Not significant
## LPS.Naive_CD8_T_cells_p38 Not significant
## LPS.Naive_CD8_T_cells_STAT1 Not significant
## LPS.Naive_CD8_T_cells_STAT3 Not significant
## LPS.Naive_CD8_T_cells_S6 Not significant
## LPS.Naive_CD8_T_cells_MAPKAPK2 Not significant
## LPS.Naive_CD8_T_cells_IkB Not significant
## LPS.Naive_CD8_T_cells_NFkB Not significant
## LPS.Naive_CD8_T_cells_ERK Not significant
## LPS.Memory_CD8_T_cells_CREB Not significant
## LPS.Memory_CD8_T_cells_STAT5 Not significant
## LPS.Memory_CD8_T_cells_p38 Not significant
## LPS.Memory_CD8_T_cells_STAT1 Not significant
## LPS.Memory_CD8_T_cells_STAT3 Not significant
## LPS.Memory_CD8_T_cells_S6 Paired only
## LPS.Memory_CD8_T_cells_MAPKAPK2 Not significant
## LPS.Memory_CD8_T_cells_IkB Not significant
## LPS.Memory_CD8_T_cells_NFkB Not significant
## LPS.Memory_CD8_T_cells_ERK Not significant
## LPS.B_cells_CREB Not significant
## LPS.B_cells_STAT5 Not significant
## LPS.B_cells_p38 Not significant
## LPS.B_cells_STAT1 Not significant
## LPS.B_cells_STAT3 Not significant
## LPS.B_cells_S6 Not significant
## LPS.B_cells_MAPKAPK2 Not significant
## LPS.B_cells_IkB Not significant
## LPS.B_cells_NFkB Not significant
## LPS.B_cells_ERK Not significant
## LPS.Classical_monocytes_CREB Not significant
## LPS.Classical_monocytes_STAT5 Not significant
## LPS.Classical_monocytes_p38 Not significant
## LPS.Classical_monocytes_STAT1 Not significant
## LPS.Classical_monocytes_STAT3 Not significant
## LPS.Classical_monocytes_S6 Not significant
## LPS.Classical_monocytes_MAPKAPK2 Not significant
## LPS.Classical_monocytes_IkB Not significant
## LPS.Classical_monocytes_NFkB Not significant
## LPS.Classical_monocytes_ERK Unpaired only
## LPS.Nonclassical_monocytes_CREB Not significant
## LPS.Nonclassical_monocytes_STAT5 Not significant
## LPS.Nonclassical_monocytes_p38 Not significant
## LPS.Nonclassical_monocytes_STAT1 Not significant
## LPS.Nonclassical_monocytes_STAT3 Not significant
## LPS.Nonclassical_monocytes_S6 Not significant
## LPS.Nonclassical_monocytes_MAPKAPK2 Not significant
## LPS.Nonclassical_monocytes_IkB Not significant
## LPS.Nonclassical_monocytes_NFkB Not significant
## LPS.Nonclassical_monocytes_ERK Not significant
## LPS.cDCs_CREB Not significant
## LPS.cDCs_STAT5 Not significant
## LPS.cDCs_p38 Not significant
## LPS.cDCs_STAT1 Not significant
## LPS.cDCs_STAT3 Not significant
## LPS.cDCs_S6 Not significant
## LPS.cDCs_MAPKAPK2 Not significant
## LPS.cDCs_IkB Not significant
## LPS.cDCs_NFkB Not significant
## LPS.cDCs_ERK Unpaired only
## LPS.pDCs_CREB Not significant
## LPS.pDCs_STAT5 Not significant
## LPS.pDCs_p38 Not significant
## LPS.pDCs_STAT1 Not significant
## LPS.pDCs_STAT3 Not significant
## LPS.pDCs_S6 Not significant
## LPS.pDCs_MAPKAPK2 Not significant
## LPS.pDCs_IkB Not significant
## LPS.pDCs_NFkB Not significant
## LPS.pDCs_ERK Not significant
## LPS.Th1_T_cells_CREB Not significant
## LPS.Th1_T_cells_STAT5 Not significant
## LPS.Th1_T_cells_p38 Not significant
## LPS.Th1_T_cells_STAT1 Not significant
## LPS.Th1_T_cells_STAT3 Not significant
## LPS.Th1_T_cells_S6 Not significant
## LPS.Th1_T_cells_MAPKAPK2 Not significant
## LPS.Th1_T_cells_IkB Not significant
## LPS.Th1_T_cells_NFkB Not significant
## LPS.Th1_T_cells_ERK Not significant
## LPS.Intermediate_monocytes_CREB Not significant
## LPS.Intermediate_monocytes_STAT5 Not significant
## LPS.Intermediate_monocytes_p38 Not significant
## LPS.Intermediate_monocytes_STAT1 Not significant
## LPS.Intermediate_monocytes_STAT3 Not significant
## LPS.Intermediate_monocytes_S6 Not significant
## LPS.Intermediate_monocytes_MAPKAPK2 Not significant
## LPS.Intermediate_monocytes_IkB Not significant
## LPS.Intermediate_monocytes_NFkB Not significant
## LPS.Intermediate_monocytes_ERK Not significant
## LPS.MDSCs_CREB Not significant
## LPS.MDSCs_STAT5 Not significant
## LPS.MDSCs_p38 Not significant
## LPS.MDSCs_STAT1 Not significant
## LPS.MDSCs_STAT3 Not significant
## LPS.MDSCs_S6 Not significant
## LPS.MDSCs_MAPKAPK2 Not significant
## LPS.MDSCs_IkB Not significant
## LPS.MDSCs_NFkB Not significant
## LPS.MDSCs_ERK Not significant
## LPS.Tregs_CREB Not significant
## LPS.Tregs_STAT5 Not significant
## LPS.Tregs_p38 Not significant
## LPS.Tregs_STAT1 Not significant
## LPS.Tregs_STAT3 Not significant
## LPS.Tregs_S6 Not significant
## LPS.Tregs_MAPKAPK2 Not significant
## LPS.Tregs_IkB Not significant
## LPS.Tregs_NFkB Not significant
## LPS.Tregs_ERK Not significant
## LPS.CD56lo_NK_cells_CREB Unpaired only
## LPS.CD56lo_NK_cells_STAT5 Not significant
## LPS.CD56lo_NK_cells_p38 Not significant
## LPS.CD56lo_NK_cells_STAT1 Not significant
## LPS.CD56lo_NK_cells_STAT3 Not significant
## LPS.CD56lo_NK_cells_S6 Not significant
## LPS.CD56lo_NK_cells_MAPKAPK2 Not significant
## LPS.CD56lo_NK_cells_IkB Not significant
## LPS.CD56lo_NK_cells_NFkB Not significant
## LPS.CD56lo_NK_cells_ERK Not significant
## LPS.CD56hi_NK_cells_CREB Not significant
## LPS.CD56hi_NK_cells_STAT5 Not significant
## LPS.CD56hi_NK_cells_p38 Not significant
## LPS.CD56hi_NK_cells_STAT1 Not significant
## LPS.CD56hi_NK_cells_STAT3 Not significant
## LPS.CD56hi_NK_cells_S6 Not significant
## LPS.CD56hi_NK_cells_MAPKAPK2 Not significant
## LPS.CD56hi_NK_cells_IkB Not significant
## LPS.CD56hi_NK_cells_NFkB Not significant
## LPS.CD56hi_NK_cells_ERK Not significant
## LPS.gd_T_cells_CREB Not significant
## LPS.gd_T_cells_STAT5 Not significant
## LPS.gd_T_cells_p38 Not significant
## LPS.gd_T_cells_STAT1 Not significant
## LPS.gd_T_cells_STAT3 Not significant
## LPS.gd_T_cells_S6 Not significant
## LPS.gd_T_cells_MAPKAPK2 Not significant
## LPS.gd_T_cells_IkB Not significant
## LPS.gd_T_cells_NFkB Not significant
## LPS.gd_T_cells_ERK Not significant
## LPS.Memory_CD4_T_cells_CREB Not significant
## LPS.Memory_CD4_T_cells_STAT5 Not significant
## LPS.Memory_CD4_T_cells_p38 Not significant
## LPS.Memory_CD4_T_cells_STAT1 Not significant
## LPS.Memory_CD4_T_cells_STAT3 Not significant
## LPS.Memory_CD4_T_cells_S6 Not significant
## LPS.Memory_CD4_T_cells_MAPKAPK2 Not significant
## LPS.Memory_CD4_T_cells_IkB Not significant
## LPS.Memory_CD4_T_cells_NFkB Not significant
## LPS.Memory_CD4_T_cells_ERK Not significant
## Cocktail.Granulocytes_CREB Not significant
## Cocktail.Granulocytes_STAT5 Not significant
## Cocktail.Granulocytes_p38 Not significant
## Cocktail.Granulocytes_STAT1 Not significant
## Cocktail.Granulocytes_STAT3 Not significant
## Cocktail.Granulocytes_S6 Not significant
## Cocktail.Granulocytes_MAPKAPK2 Not significant
## Cocktail.Granulocytes_IkB Not significant
## Cocktail.Granulocytes_NFkB Not significant
## Cocktail.Granulocytes_ERK Not significant
## Cocktail.CD8_T_cells_CREB Not significant
## Cocktail.CD8_T_cells_STAT5 Unpaired only
## Cocktail.CD8_T_cells_p38 Not significant
## Cocktail.CD8_T_cells_STAT1 Not significant
## Cocktail.CD8_T_cells_STAT3 Not significant
## Cocktail.CD8_T_cells_S6 Not significant
## Cocktail.CD8_T_cells_MAPKAPK2 Not significant
## Cocktail.CD8_T_cells_IkB Not significant
## Cocktail.CD8_T_cells_NFkB Not significant
## Cocktail.CD8_T_cells_ERK Not significant
## Cocktail.CD4_T_cells_CREB Not significant
## Cocktail.CD4_T_cells_STAT5 Unpaired only
## Cocktail.CD4_T_cells_p38 Not significant
## Cocktail.CD4_T_cells_STAT1 Both
## Cocktail.CD4_T_cells_STAT3 Not significant
## Cocktail.CD4_T_cells_S6 Not significant
## Cocktail.CD4_T_cells_MAPKAPK2 Not significant
## Cocktail.CD4_T_cells_IkB Not significant
## Cocktail.CD4_T_cells_NFkB Not significant
## Cocktail.CD4_T_cells_ERK Not significant
## Cocktail.Naive_CD4_T_cells_CREB Not significant
## Cocktail.Naive_CD4_T_cells_STAT5 Both
## Cocktail.Naive_CD4_T_cells_p38 Not significant
## Cocktail.Naive_CD4_T_cells_STAT1 Both
## Cocktail.Naive_CD4_T_cells_STAT3 Not significant
## Cocktail.Naive_CD4_T_cells_S6 Not significant
## Cocktail.Naive_CD4_T_cells_MAPKAPK2 Not significant
## Cocktail.Naive_CD4_T_cells_IkB Not significant
## Cocktail.Naive_CD4_T_cells_NFkB Not significant
## Cocktail.Naive_CD4_T_cells_ERK Not significant
## Cocktail.Naive_CD8_T_cells_CREB Not significant
## Cocktail.Naive_CD8_T_cells_STAT5 Both
## Cocktail.Naive_CD8_T_cells_p38 Not significant
## Cocktail.Naive_CD8_T_cells_STAT1 Not significant
## Cocktail.Naive_CD8_T_cells_STAT3 Not significant
## Cocktail.Naive_CD8_T_cells_S6 Not significant
## Cocktail.Naive_CD8_T_cells_MAPKAPK2 Not significant
## Cocktail.Naive_CD8_T_cells_IkB Not significant
## Cocktail.Naive_CD8_T_cells_NFkB Not significant
## Cocktail.Naive_CD8_T_cells_ERK Not significant
## Cocktail.Memory_CD8_T_cells_CREB Not significant
## Cocktail.Memory_CD8_T_cells_STAT5 Not significant
## Cocktail.Memory_CD8_T_cells_p38 Not significant
## Cocktail.Memory_CD8_T_cells_STAT1 Not significant
## Cocktail.Memory_CD8_T_cells_STAT3 Not significant
## Cocktail.Memory_CD8_T_cells_S6 Not significant
## Cocktail.Memory_CD8_T_cells_MAPKAPK2 Not significant
## Cocktail.Memory_CD8_T_cells_IkB Not significant
## Cocktail.Memory_CD8_T_cells_NFkB Not significant
## Cocktail.Memory_CD8_T_cells_ERK Not significant
## Cocktail.B_cells_CREB Not significant
## Cocktail.B_cells_STAT5 Not significant
## Cocktail.B_cells_p38 Not significant
## Cocktail.B_cells_STAT1 Not significant
## Cocktail.B_cells_STAT3 Not significant
## Cocktail.B_cells_S6 Not significant
## Cocktail.B_cells_MAPKAPK2 Not significant
## Cocktail.B_cells_IkB Not significant
## Cocktail.B_cells_NFkB Not significant
## Cocktail.B_cells_ERK Not significant
## Cocktail.Classical_monocytes_CREB Not significant
## Cocktail.Classical_monocytes_STAT5 Not significant
## Cocktail.Classical_monocytes_p38 Not significant
## Cocktail.Classical_monocytes_STAT1 Both
## Cocktail.Classical_monocytes_STAT3 Both
## Cocktail.Classical_monocytes_S6 Not significant
## Cocktail.Classical_monocytes_MAPKAPK2 Not significant
## Cocktail.Classical_monocytes_IkB Not significant
## Cocktail.Classical_monocytes_NFkB Not significant
## Cocktail.Classical_monocytes_ERK Not significant
## Cocktail.Nonclassical_monocytes_CREB Not significant
## Cocktail.Nonclassical_monocytes_STAT5 Not significant
## Cocktail.Nonclassical_monocytes_p38 Not significant
## Cocktail.Nonclassical_monocytes_STAT1 Not significant
## Cocktail.Nonclassical_monocytes_STAT3 Not significant
## Cocktail.Nonclassical_monocytes_S6 Not significant
## Cocktail.Nonclassical_monocytes_MAPKAPK2 Not significant
## Cocktail.Nonclassical_monocytes_IkB Not significant
## Cocktail.Nonclassical_monocytes_NFkB Not significant
## Cocktail.Nonclassical_monocytes_ERK Not significant
## Cocktail.cDCs_CREB Not significant
## Cocktail.cDCs_STAT5 Not significant
## Cocktail.cDCs_p38 Not significant
## Cocktail.cDCs_STAT1 Both
## Cocktail.cDCs_STAT3 Both
## Cocktail.cDCs_S6 Not significant
## Cocktail.cDCs_MAPKAPK2 Not significant
## Cocktail.cDCs_IkB Not significant
## Cocktail.cDCs_NFkB Not significant
## Cocktail.cDCs_ERK Not significant
## Cocktail.pDCs_CREB Not significant
## Cocktail.pDCs_STAT5 Not significant
## Cocktail.pDCs_p38 Not significant
## Cocktail.pDCs_STAT1 Not significant
## Cocktail.pDCs_STAT3 Not significant
## Cocktail.pDCs_S6 Not significant
## Cocktail.pDCs_MAPKAPK2 Not significant
## Cocktail.pDCs_IkB Not significant
## Cocktail.pDCs_NFkB Not significant
## Cocktail.pDCs_ERK Not significant
## Cocktail.Th1_T_cells_CREB Not significant
## Cocktail.Th1_T_cells_STAT5 Not significant
## Cocktail.Th1_T_cells_p38 Not significant
## Cocktail.Th1_T_cells_STAT1 Not significant
## Cocktail.Th1_T_cells_STAT3 Not significant
## Cocktail.Th1_T_cells_S6 Not significant
## Cocktail.Th1_T_cells_MAPKAPK2 Not significant
## Cocktail.Th1_T_cells_IkB Not significant
## Cocktail.Th1_T_cells_NFkB Not significant
## Cocktail.Th1_T_cells_ERK Not significant
## Cocktail.Intermediate_monocytes_CREB Not significant
## Cocktail.Intermediate_monocytes_STAT5 Not significant
## Cocktail.Intermediate_monocytes_p38 Not significant
## Cocktail.Intermediate_monocytes_STAT1 Both
## Cocktail.Intermediate_monocytes_STAT3 Not significant
## Cocktail.Intermediate_monocytes_S6 Not significant
## Cocktail.Intermediate_monocytes_MAPKAPK2 Not significant
## Cocktail.Intermediate_monocytes_IkB Not significant
## Cocktail.Intermediate_monocytes_NFkB Not significant
## Cocktail.Intermediate_monocytes_ERK Not significant
## Cocktail.MDSCs_CREB Not significant
## Cocktail.MDSCs_STAT5 Not significant
## Cocktail.MDSCs_p38 Not significant
## Cocktail.MDSCs_STAT1 Not significant
## Cocktail.MDSCs_STAT3 Not significant
## Cocktail.MDSCs_S6 Not significant
## Cocktail.MDSCs_MAPKAPK2 Not significant
## Cocktail.MDSCs_IkB Not significant
## Cocktail.MDSCs_NFkB Not significant
## Cocktail.MDSCs_ERK Not significant
## Cocktail.Tregs_CREB Not significant
## Cocktail.Tregs_STAT5 Not significant
## Cocktail.Tregs_p38 Not significant
## Cocktail.Tregs_STAT1 Both
## Cocktail.Tregs_STAT3 Not significant
## Cocktail.Tregs_S6 Not significant
## Cocktail.Tregs_MAPKAPK2 Not significant
## Cocktail.Tregs_IkB Not significant
## Cocktail.Tregs_NFkB Not significant
## Cocktail.Tregs_ERK Not significant
## Cocktail.CD56lo_NK_cells_CREB Not significant
## Cocktail.CD56lo_NK_cells_STAT5 Not significant
## Cocktail.CD56lo_NK_cells_p38 Not significant
## Cocktail.CD56lo_NK_cells_STAT1 Both
## Cocktail.CD56lo_NK_cells_STAT3 Not significant
## Cocktail.CD56lo_NK_cells_S6 Not significant
## Cocktail.CD56lo_NK_cells_MAPKAPK2 Not significant
## Cocktail.CD56lo_NK_cells_IkB Not significant
## Cocktail.CD56lo_NK_cells_NFkB Not significant
## Cocktail.CD56lo_NK_cells_ERK Not significant
## Cocktail.CD56hi_NK_cells_CREB Not significant
## Cocktail.CD56hi_NK_cells_STAT5 Not significant
## Cocktail.CD56hi_NK_cells_p38 Not significant
## Cocktail.CD56hi_NK_cells_STAT1 Both
## Cocktail.CD56hi_NK_cells_STAT3 Not significant
## Cocktail.CD56hi_NK_cells_S6 Not significant
## Cocktail.CD56hi_NK_cells_MAPKAPK2 Both
## Cocktail.CD56hi_NK_cells_IkB Not significant
## Cocktail.CD56hi_NK_cells_NFkB Not significant
## Cocktail.CD56hi_NK_cells_ERK Not significant
## Cocktail.gd_T_cells_CREB Not significant
## Cocktail.gd_T_cells_STAT5 Not significant
## Cocktail.gd_T_cells_p38 Not significant
## Cocktail.gd_T_cells_STAT1 Not significant
## Cocktail.gd_T_cells_STAT3 Not significant
## Cocktail.gd_T_cells_S6 Not significant
## Cocktail.gd_T_cells_MAPKAPK2 Not significant
## Cocktail.gd_T_cells_IkB Not significant
## Cocktail.gd_T_cells_NFkB Not significant
## Cocktail.gd_T_cells_ERK Not significant
## Cocktail.Memory_CD4_T_cells_CREB Not significant
## Cocktail.Memory_CD4_T_cells_STAT5 Not significant
## Cocktail.Memory_CD4_T_cells_p38 Not significant
## Cocktail.Memory_CD4_T_cells_STAT1 Not significant
## Cocktail.Memory_CD4_T_cells_STAT3 Not significant
## Cocktail.Memory_CD4_T_cells_S6 Not significant
## Cocktail.Memory_CD4_T_cells_MAPKAPK2 Not significant
## Cocktail.Memory_CD4_T_cells_IkB Not significant
## Cocktail.Memory_CD4_T_cells_NFkB Not significant
## Cocktail.Memory_CD4_T_cells_ERK Not significant
## Significance_SAM
## LPS.Granulocytes_CREB Both
## LPS.Granulocytes_STAT5 Not significant
## LPS.Granulocytes_p38 Both
## LPS.Granulocytes_STAT1 Both
## LPS.Granulocytes_STAT3 Not significant
## LPS.Granulocytes_S6 Not significant
## LPS.Granulocytes_MAPKAPK2 Both
## LPS.Granulocytes_IkB Not significant
## LPS.Granulocytes_NFkB Both
## LPS.Granulocytes_ERK Not significant
## LPS.CD8_T_cells_CREB Not significant
## LPS.CD8_T_cells_STAT5 Not significant
## LPS.CD8_T_cells_p38 Not significant
## LPS.CD8_T_cells_STAT1 Not significant
## LPS.CD8_T_cells_STAT3 Not significant
## LPS.CD8_T_cells_S6 Not significant
## LPS.CD8_T_cells_MAPKAPK2 Not significant
## LPS.CD8_T_cells_IkB Not significant
## LPS.CD8_T_cells_NFkB Not significant
## LPS.CD8_T_cells_ERK Not significant
## LPS.CD4_T_cells_CREB Not significant
## LPS.CD4_T_cells_STAT5 Not significant
## LPS.CD4_T_cells_p38 Not significant
## LPS.CD4_T_cells_STAT1 Not significant
## LPS.CD4_T_cells_STAT3 Not significant
## LPS.CD4_T_cells_S6 Not significant
## LPS.CD4_T_cells_MAPKAPK2 Not significant
## LPS.CD4_T_cells_IkB Not significant
## LPS.CD4_T_cells_NFkB Not significant
## LPS.CD4_T_cells_ERK Not significant
## LPS.Naive_CD4_T_cells_CREB Not significant
## LPS.Naive_CD4_T_cells_STAT5 Not significant
## LPS.Naive_CD4_T_cells_p38 Not significant
## LPS.Naive_CD4_T_cells_STAT1 Not significant
## LPS.Naive_CD4_T_cells_STAT3 Not significant
## LPS.Naive_CD4_T_cells_S6 Not significant
## LPS.Naive_CD4_T_cells_MAPKAPK2 Not significant
## LPS.Naive_CD4_T_cells_IkB Unpaired only
## LPS.Naive_CD4_T_cells_NFkB Not significant
## LPS.Naive_CD4_T_cells_ERK Both
## LPS.Naive_CD8_T_cells_CREB Not significant
## LPS.Naive_CD8_T_cells_STAT5 Not significant
## LPS.Naive_CD8_T_cells_p38 Not significant
## LPS.Naive_CD8_T_cells_STAT1 Not significant
## LPS.Naive_CD8_T_cells_STAT3 Not significant
## LPS.Naive_CD8_T_cells_S6 Not significant
## LPS.Naive_CD8_T_cells_MAPKAPK2 Not significant
## LPS.Naive_CD8_T_cells_IkB Unpaired only
## LPS.Naive_CD8_T_cells_NFkB Not significant
## LPS.Naive_CD8_T_cells_ERK Not significant
## LPS.Memory_CD8_T_cells_CREB Both
## LPS.Memory_CD8_T_cells_STAT5 Not significant
## LPS.Memory_CD8_T_cells_p38 Unpaired only
## LPS.Memory_CD8_T_cells_STAT1 Not significant
## LPS.Memory_CD8_T_cells_STAT3 Not significant
## LPS.Memory_CD8_T_cells_S6 Both
## LPS.Memory_CD8_T_cells_MAPKAPK2 Not significant
## LPS.Memory_CD8_T_cells_IkB Not significant
## LPS.Memory_CD8_T_cells_NFkB Not significant
## LPS.Memory_CD8_T_cells_ERK Not significant
## LPS.B_cells_CREB Not significant
## LPS.B_cells_STAT5 Both
## LPS.B_cells_p38 Not significant
## LPS.B_cells_STAT1 Not significant
## LPS.B_cells_STAT3 Not significant
## LPS.B_cells_S6 Unpaired only
## LPS.B_cells_MAPKAPK2 Not significant
## LPS.B_cells_IkB Not significant
## LPS.B_cells_NFkB Not significant
## LPS.B_cells_ERK Both
## LPS.Classical_monocytes_CREB Not significant
## LPS.Classical_monocytes_STAT5 Not significant
## LPS.Classical_monocytes_p38 Not significant
## LPS.Classical_monocytes_STAT1 Not significant
## LPS.Classical_monocytes_STAT3 Not significant
## LPS.Classical_monocytes_S6 Not significant
## LPS.Classical_monocytes_MAPKAPK2 Both
## LPS.Classical_monocytes_IkB Not significant
## LPS.Classical_monocytes_NFkB Not significant
## LPS.Classical_monocytes_ERK Both
## LPS.Nonclassical_monocytes_CREB Both
## LPS.Nonclassical_monocytes_STAT5 Not significant
## LPS.Nonclassical_monocytes_p38 Not significant
## LPS.Nonclassical_monocytes_STAT1 Not significant
## LPS.Nonclassical_monocytes_STAT3 Not significant
## LPS.Nonclassical_monocytes_S6 Both
## LPS.Nonclassical_monocytes_MAPKAPK2 Not significant
## LPS.Nonclassical_monocytes_IkB Not significant
## LPS.Nonclassical_monocytes_NFkB Not significant
## LPS.Nonclassical_monocytes_ERK Not significant
## LPS.cDCs_CREB Both
## LPS.cDCs_STAT5 Not significant
## LPS.cDCs_p38 Paired only
## LPS.cDCs_STAT1 Not significant
## LPS.cDCs_STAT3 Not significant
## LPS.cDCs_S6 Unpaired only
## LPS.cDCs_MAPKAPK2 Both
## LPS.cDCs_IkB Not significant
## LPS.cDCs_NFkB Not significant
## LPS.cDCs_ERK Both
## LPS.pDCs_CREB Unpaired only
## LPS.pDCs_STAT5 Not significant
## LPS.pDCs_p38 Not significant
## LPS.pDCs_STAT1 Not significant
## LPS.pDCs_STAT3 Both
## LPS.pDCs_S6 Both
## LPS.pDCs_MAPKAPK2 Not significant
## LPS.pDCs_IkB Not significant
## LPS.pDCs_NFkB Not significant
## LPS.pDCs_ERK Both
## LPS.Th1_T_cells_CREB Both
## LPS.Th1_T_cells_STAT5 Both
## LPS.Th1_T_cells_p38 Both
## LPS.Th1_T_cells_STAT1 Both
## LPS.Th1_T_cells_STAT3 Both
## LPS.Th1_T_cells_S6 Both
## LPS.Th1_T_cells_MAPKAPK2 Both
## LPS.Th1_T_cells_IkB Both
## LPS.Th1_T_cells_NFkB Not significant
## LPS.Th1_T_cells_ERK Both
## LPS.Intermediate_monocytes_CREB Both
## LPS.Intermediate_monocytes_STAT5 Not significant
## LPS.Intermediate_monocytes_p38 Not significant
## LPS.Intermediate_monocytes_STAT1 Not significant
## LPS.Intermediate_monocytes_STAT3 Unpaired only
## LPS.Intermediate_monocytes_S6 Both
## LPS.Intermediate_monocytes_MAPKAPK2 Not significant
## LPS.Intermediate_monocytes_IkB Paired only
## LPS.Intermediate_monocytes_NFkB Not significant
## LPS.Intermediate_monocytes_ERK Both
## LPS.MDSCs_CREB Not significant
## LPS.MDSCs_STAT5 Not significant
## LPS.MDSCs_p38 Not significant
## LPS.MDSCs_STAT1 Not significant
## LPS.MDSCs_STAT3 Not significant
## LPS.MDSCs_S6 Not significant
## LPS.MDSCs_MAPKAPK2 Not significant
## LPS.MDSCs_IkB Not significant
## LPS.MDSCs_NFkB Not significant
## LPS.MDSCs_ERK Not significant
## LPS.Tregs_CREB Both
## LPS.Tregs_STAT5 Not significant
## LPS.Tregs_p38 Both
## LPS.Tregs_STAT1 Both
## LPS.Tregs_STAT3 Not significant
## LPS.Tregs_S6 Not significant
## LPS.Tregs_MAPKAPK2 Not significant
## LPS.Tregs_IkB Not significant
## LPS.Tregs_NFkB Not significant
## LPS.Tregs_ERK Both
## LPS.CD56lo_NK_cells_CREB Both
## LPS.CD56lo_NK_cells_STAT5 Not significant
## LPS.CD56lo_NK_cells_p38 Not significant
## LPS.CD56lo_NK_cells_STAT1 Unpaired only
## LPS.CD56lo_NK_cells_STAT3 Not significant
## LPS.CD56lo_NK_cells_S6 Not significant
## LPS.CD56lo_NK_cells_MAPKAPK2 Not significant
## LPS.CD56lo_NK_cells_IkB Not significant
## LPS.CD56lo_NK_cells_NFkB Not significant
## LPS.CD56lo_NK_cells_ERK Not significant
## LPS.CD56hi_NK_cells_CREB Both
## LPS.CD56hi_NK_cells_STAT5 Not significant
## LPS.CD56hi_NK_cells_p38 Not significant
## LPS.CD56hi_NK_cells_STAT1 Not significant
## LPS.CD56hi_NK_cells_STAT3 Not significant
## LPS.CD56hi_NK_cells_S6 Not significant
## LPS.CD56hi_NK_cells_MAPKAPK2 Not significant
## LPS.CD56hi_NK_cells_IkB Not significant
## LPS.CD56hi_NK_cells_NFkB Not significant
## LPS.CD56hi_NK_cells_ERK Both
## LPS.gd_T_cells_CREB Not significant
## LPS.gd_T_cells_STAT5 Not significant
## LPS.gd_T_cells_p38 Not significant
## LPS.gd_T_cells_STAT1 Not significant
## LPS.gd_T_cells_STAT3 Not significant
## LPS.gd_T_cells_S6 Unpaired only
## LPS.gd_T_cells_MAPKAPK2 Not significant
## LPS.gd_T_cells_IkB Not significant
## LPS.gd_T_cells_NFkB Not significant
## LPS.gd_T_cells_ERK Not significant
## LPS.Memory_CD4_T_cells_CREB Not significant
## LPS.Memory_CD4_T_cells_STAT5 Not significant
## LPS.Memory_CD4_T_cells_p38 Both
## LPS.Memory_CD4_T_cells_STAT1 Unpaired only
## LPS.Memory_CD4_T_cells_STAT3 Not significant
## LPS.Memory_CD4_T_cells_S6 Not significant
## LPS.Memory_CD4_T_cells_MAPKAPK2 Not significant
## LPS.Memory_CD4_T_cells_IkB Not significant
## LPS.Memory_CD4_T_cells_NFkB Not significant
## LPS.Memory_CD4_T_cells_ERK Not significant
## Cocktail.Granulocytes_CREB Not significant
## Cocktail.Granulocytes_STAT5 Not significant
## Cocktail.Granulocytes_p38 Paired only
## Cocktail.Granulocytes_STAT1 Both
## Cocktail.Granulocytes_STAT3 Not significant
## Cocktail.Granulocytes_S6 Not significant
## Cocktail.Granulocytes_MAPKAPK2 Not significant
## Cocktail.Granulocytes_IkB Not significant
## Cocktail.Granulocytes_NFkB Both
## Cocktail.Granulocytes_ERK Not significant
## Cocktail.CD8_T_cells_CREB Not significant
## Cocktail.CD8_T_cells_STAT5 Both
## Cocktail.CD8_T_cells_p38 Not significant
## Cocktail.CD8_T_cells_STAT1 Not significant
## Cocktail.CD8_T_cells_STAT3 Both
## Cocktail.CD8_T_cells_S6 Not significant
## Cocktail.CD8_T_cells_MAPKAPK2 Not significant
## Cocktail.CD8_T_cells_IkB Not significant
## Cocktail.CD8_T_cells_NFkB Not significant
## Cocktail.CD8_T_cells_ERK Not significant
## Cocktail.CD4_T_cells_CREB Not significant
## Cocktail.CD4_T_cells_STAT5 Both
## Cocktail.CD4_T_cells_p38 Not significant
## Cocktail.CD4_T_cells_STAT1 Both
## Cocktail.CD4_T_cells_STAT3 Not significant
## Cocktail.CD4_T_cells_S6 Not significant
## Cocktail.CD4_T_cells_MAPKAPK2 Not significant
## Cocktail.CD4_T_cells_IkB Not significant
## Cocktail.CD4_T_cells_NFkB Not significant
## Cocktail.CD4_T_cells_ERK Not significant
## Cocktail.Naive_CD4_T_cells_CREB Not significant
## Cocktail.Naive_CD4_T_cells_STAT5 Both
## Cocktail.Naive_CD4_T_cells_p38 Not significant
## Cocktail.Naive_CD4_T_cells_STAT1 Both
## Cocktail.Naive_CD4_T_cells_STAT3 Not significant
## Cocktail.Naive_CD4_T_cells_S6 Not significant
## Cocktail.Naive_CD4_T_cells_MAPKAPK2 Not significant
## Cocktail.Naive_CD4_T_cells_IkB Not significant
## Cocktail.Naive_CD4_T_cells_NFkB Not significant
## Cocktail.Naive_CD4_T_cells_ERK Not significant
## Cocktail.Naive_CD8_T_cells_CREB Not significant
## Cocktail.Naive_CD8_T_cells_STAT5 Both
## Cocktail.Naive_CD8_T_cells_p38 Not significant
## Cocktail.Naive_CD8_T_cells_STAT1 Both
## Cocktail.Naive_CD8_T_cells_STAT3 Not significant
## Cocktail.Naive_CD8_T_cells_S6 Not significant
## Cocktail.Naive_CD8_T_cells_MAPKAPK2 Not significant
## Cocktail.Naive_CD8_T_cells_IkB Not significant
## Cocktail.Naive_CD8_T_cells_NFkB Not significant
## Cocktail.Naive_CD8_T_cells_ERK Not significant
## Cocktail.Memory_CD8_T_cells_CREB Both
## Cocktail.Memory_CD8_T_cells_STAT5 Not significant
## Cocktail.Memory_CD8_T_cells_p38 Not significant
## Cocktail.Memory_CD8_T_cells_STAT1 Not significant
## Cocktail.Memory_CD8_T_cells_STAT3 Both
## Cocktail.Memory_CD8_T_cells_S6 Both
## Cocktail.Memory_CD8_T_cells_MAPKAPK2 Not significant
## Cocktail.Memory_CD8_T_cells_IkB Not significant
## Cocktail.Memory_CD8_T_cells_NFkB Not significant
## Cocktail.Memory_CD8_T_cells_ERK Not significant
## Cocktail.B_cells_CREB Not significant
## Cocktail.B_cells_STAT5 Not significant
## Cocktail.B_cells_p38 Not significant
## Cocktail.B_cells_STAT1 Both
## Cocktail.B_cells_STAT3 Not significant
## Cocktail.B_cells_S6 Not significant
## Cocktail.B_cells_MAPKAPK2 Not significant
## Cocktail.B_cells_IkB Not significant
## Cocktail.B_cells_NFkB Not significant
## Cocktail.B_cells_ERK Not significant
## Cocktail.Classical_monocytes_CREB Not significant
## Cocktail.Classical_monocytes_STAT5 Not significant
## Cocktail.Classical_monocytes_p38 Not significant
## Cocktail.Classical_monocytes_STAT1 Both
## Cocktail.Classical_monocytes_STAT3 Both
## Cocktail.Classical_monocytes_S6 Not significant
## Cocktail.Classical_monocytes_MAPKAPK2 Not significant
## Cocktail.Classical_monocytes_IkB Not significant
## Cocktail.Classical_monocytes_NFkB Not significant
## Cocktail.Classical_monocytes_ERK Not significant
## Cocktail.Nonclassical_monocytes_CREB Both
## Cocktail.Nonclassical_monocytes_STAT5 Not significant
## Cocktail.Nonclassical_monocytes_p38 Not significant
## Cocktail.Nonclassical_monocytes_STAT1 Paired only
## Cocktail.Nonclassical_monocytes_STAT3 Not significant
## Cocktail.Nonclassical_monocytes_S6 Both
## Cocktail.Nonclassical_monocytes_MAPKAPK2 Not significant
## Cocktail.Nonclassical_monocytes_IkB Not significant
## Cocktail.Nonclassical_monocytes_NFkB Not significant
## Cocktail.Nonclassical_monocytes_ERK Not significant
## Cocktail.cDCs_CREB Not significant
## Cocktail.cDCs_STAT5 Not significant
## Cocktail.cDCs_p38 Not significant
## Cocktail.cDCs_STAT1 Both
## Cocktail.cDCs_STAT3 Both
## Cocktail.cDCs_S6 Not significant
## Cocktail.cDCs_MAPKAPK2 Not significant
## Cocktail.cDCs_IkB Not significant
## Cocktail.cDCs_NFkB Not significant
## Cocktail.cDCs_ERK Not significant
## Cocktail.pDCs_CREB Not significant
## Cocktail.pDCs_STAT5 Both
## Cocktail.pDCs_p38 Not significant
## Cocktail.pDCs_STAT1 Both
## Cocktail.pDCs_STAT3 Both
## Cocktail.pDCs_S6 Not significant
## Cocktail.pDCs_MAPKAPK2 Not significant
## Cocktail.pDCs_IkB Not significant
## Cocktail.pDCs_NFkB Not significant
## Cocktail.pDCs_ERK Both
## Cocktail.Th1_T_cells_CREB Not significant
## Cocktail.Th1_T_cells_STAT5 Not significant
## Cocktail.Th1_T_cells_p38 Not significant
## Cocktail.Th1_T_cells_STAT1 Not significant
## Cocktail.Th1_T_cells_STAT3 Not significant
## Cocktail.Th1_T_cells_S6 Not significant
## Cocktail.Th1_T_cells_MAPKAPK2 Not significant
## Cocktail.Th1_T_cells_IkB Not significant
## Cocktail.Th1_T_cells_NFkB Not significant
## Cocktail.Th1_T_cells_ERK Both
## Cocktail.Intermediate_monocytes_CREB Both
## Cocktail.Intermediate_monocytes_STAT5 Not significant
## Cocktail.Intermediate_monocytes_p38 Not significant
## Cocktail.Intermediate_monocytes_STAT1 Both
## Cocktail.Intermediate_monocytes_STAT3 Both
## Cocktail.Intermediate_monocytes_S6 Both
## Cocktail.Intermediate_monocytes_MAPKAPK2 Both
## Cocktail.Intermediate_monocytes_IkB Not significant
## Cocktail.Intermediate_monocytes_NFkB Not significant
## Cocktail.Intermediate_monocytes_ERK Not significant
## Cocktail.MDSCs_CREB Not significant
## Cocktail.MDSCs_STAT5 Not significant
## Cocktail.MDSCs_p38 Not significant
## Cocktail.MDSCs_STAT1 Both
## Cocktail.MDSCs_STAT3 Both
## Cocktail.MDSCs_S6 Not significant
## Cocktail.MDSCs_MAPKAPK2 Not significant
## Cocktail.MDSCs_IkB Not significant
## Cocktail.MDSCs_NFkB Not significant
## Cocktail.MDSCs_ERK Not significant
## Cocktail.Tregs_CREB Not significant
## Cocktail.Tregs_STAT5 Not significant
## Cocktail.Tregs_p38 Not significant
## Cocktail.Tregs_STAT1 Both
## Cocktail.Tregs_STAT3 Not significant
## Cocktail.Tregs_S6 Not significant
## Cocktail.Tregs_MAPKAPK2 Not significant
## Cocktail.Tregs_IkB Not significant
## Cocktail.Tregs_NFkB Not significant
## Cocktail.Tregs_ERK Not significant
## Cocktail.CD56lo_NK_cells_CREB Both
## Cocktail.CD56lo_NK_cells_STAT5 Not significant
## Cocktail.CD56lo_NK_cells_p38 Not significant
## Cocktail.CD56lo_NK_cells_STAT1 Both
## Cocktail.CD56lo_NK_cells_STAT3 Both
## Cocktail.CD56lo_NK_cells_S6 Paired only
## Cocktail.CD56lo_NK_cells_MAPKAPK2 Not significant
## Cocktail.CD56lo_NK_cells_IkB Not significant
## Cocktail.CD56lo_NK_cells_NFkB Not significant
## Cocktail.CD56lo_NK_cells_ERK Paired only
## Cocktail.CD56hi_NK_cells_CREB Not significant
## Cocktail.CD56hi_NK_cells_STAT5 Not significant
## Cocktail.CD56hi_NK_cells_p38 Not significant
## Cocktail.CD56hi_NK_cells_STAT1 Both
## Cocktail.CD56hi_NK_cells_STAT3 Not significant
## Cocktail.CD56hi_NK_cells_S6 Not significant
## Cocktail.CD56hi_NK_cells_MAPKAPK2 Both
## Cocktail.CD56hi_NK_cells_IkB Not significant
## Cocktail.CD56hi_NK_cells_NFkB Not significant
## Cocktail.CD56hi_NK_cells_ERK Not significant
## Cocktail.gd_T_cells_CREB Unpaired only
## Cocktail.gd_T_cells_STAT5 Both
## Cocktail.gd_T_cells_p38 Not significant
## Cocktail.gd_T_cells_STAT1 Both
## Cocktail.gd_T_cells_STAT3 Paired only
## Cocktail.gd_T_cells_S6 Not significant
## Cocktail.gd_T_cells_MAPKAPK2 Not significant
## Cocktail.gd_T_cells_IkB Not significant
## Cocktail.gd_T_cells_NFkB Not significant
## Cocktail.gd_T_cells_ERK Not significant
## Cocktail.Memory_CD4_T_cells_CREB Not significant
## Cocktail.Memory_CD4_T_cells_STAT5 Both
## Cocktail.Memory_CD4_T_cells_p38 Not significant
## Cocktail.Memory_CD4_T_cells_STAT1 Both
## Cocktail.Memory_CD4_T_cells_STAT3 Not significant
## Cocktail.Memory_CD4_T_cells_S6 Not significant
## Cocktail.Memory_CD4_T_cells_MAPKAPK2 Not significant
## Cocktail.Memory_CD4_T_cells_IkB Not significant
## Cocktail.Memory_CD4_T_cells_NFkB Not significant
## Cocktail.Memory_CD4_T_cells_ERK Not significant
## Features
## LPS.Granulocytes_CREB LPS.Granulocytes_CREB
## LPS.Granulocytes_STAT5 LPS.Granulocytes_STAT5
## LPS.Granulocytes_p38 LPS.Granulocytes_p38
## LPS.Granulocytes_STAT1 LPS.Granulocytes_STAT1
## LPS.Granulocytes_STAT3 LPS.Granulocytes_STAT3
## LPS.Granulocytes_S6 LPS.Granulocytes_S6
## LPS.Granulocytes_MAPKAPK2 LPS.Granulocytes_MAPKAPK2
## LPS.Granulocytes_IkB LPS.Granulocytes_IkB
## LPS.Granulocytes_NFkB LPS.Granulocytes_NFkB
## LPS.Granulocytes_ERK LPS.Granulocytes_ERK
## LPS.CD8_T_cells_CREB LPS.CD8_T_cells_CREB
## LPS.CD8_T_cells_STAT5 LPS.CD8_T_cells_STAT5
## LPS.CD8_T_cells_p38 LPS.CD8_T_cells_p38
## LPS.CD8_T_cells_STAT1 LPS.CD8_T_cells_STAT1
## LPS.CD8_T_cells_STAT3 LPS.CD8_T_cells_STAT3
## LPS.CD8_T_cells_S6 LPS.CD8_T_cells_S6
## LPS.CD8_T_cells_MAPKAPK2 LPS.CD8_T_cells_MAPKAPK2
## LPS.CD8_T_cells_IkB LPS.CD8_T_cells_IkB
## LPS.CD8_T_cells_NFkB LPS.CD8_T_cells_NFkB
## LPS.CD8_T_cells_ERK LPS.CD8_T_cells_ERK
## LPS.CD4_T_cells_CREB LPS.CD4_T_cells_CREB
## LPS.CD4_T_cells_STAT5 LPS.CD4_T_cells_STAT5
## LPS.CD4_T_cells_p38 LPS.CD4_T_cells_p38
## LPS.CD4_T_cells_STAT1 LPS.CD4_T_cells_STAT1
## LPS.CD4_T_cells_STAT3 LPS.CD4_T_cells_STAT3
## LPS.CD4_T_cells_S6 LPS.CD4_T_cells_S6
## LPS.CD4_T_cells_MAPKAPK2 LPS.CD4_T_cells_MAPKAPK2
## LPS.CD4_T_cells_IkB LPS.CD4_T_cells_IkB
## LPS.CD4_T_cells_NFkB LPS.CD4_T_cells_NFkB
## LPS.CD4_T_cells_ERK LPS.CD4_T_cells_ERK
## LPS.Naive_CD4_T_cells_CREB LPS.Naive_CD4_T_cells_CREB
## LPS.Naive_CD4_T_cells_STAT5 LPS.Naive_CD4_T_cells_STAT5
## LPS.Naive_CD4_T_cells_p38 LPS.Naive_CD4_T_cells_p38
## LPS.Naive_CD4_T_cells_STAT1 LPS.Naive_CD4_T_cells_STAT1
## LPS.Naive_CD4_T_cells_STAT3 LPS.Naive_CD4_T_cells_STAT3
## LPS.Naive_CD4_T_cells_S6 LPS.Naive_CD4_T_cells_S6
## LPS.Naive_CD4_T_cells_MAPKAPK2 LPS.Naive_CD4_T_cells_MAPKAPK2
## LPS.Naive_CD4_T_cells_IkB LPS.Naive_CD4_T_cells_IkB
## LPS.Naive_CD4_T_cells_NFkB LPS.Naive_CD4_T_cells_NFkB
## LPS.Naive_CD4_T_cells_ERK LPS.Naive_CD4_T_cells_ERK
## LPS.Naive_CD8_T_cells_CREB LPS.Naive_CD8_T_cells_CREB
## LPS.Naive_CD8_T_cells_STAT5 LPS.Naive_CD8_T_cells_STAT5
## LPS.Naive_CD8_T_cells_p38 LPS.Naive_CD8_T_cells_p38
## LPS.Naive_CD8_T_cells_STAT1 LPS.Naive_CD8_T_cells_STAT1
## LPS.Naive_CD8_T_cells_STAT3 LPS.Naive_CD8_T_cells_STAT3
## LPS.Naive_CD8_T_cells_S6 LPS.Naive_CD8_T_cells_S6
## LPS.Naive_CD8_T_cells_MAPKAPK2 LPS.Naive_CD8_T_cells_MAPKAPK2
## LPS.Naive_CD8_T_cells_IkB LPS.Naive_CD8_T_cells_IkB
## LPS.Naive_CD8_T_cells_NFkB LPS.Naive_CD8_T_cells_NFkB
## LPS.Naive_CD8_T_cells_ERK LPS.Naive_CD8_T_cells_ERK
## LPS.Memory_CD8_T_cells_CREB LPS.Memory_CD8_T_cells_CREB
## LPS.Memory_CD8_T_cells_STAT5 LPS.Memory_CD8_T_cells_STAT5
## LPS.Memory_CD8_T_cells_p38 LPS.Memory_CD8_T_cells_p38
## LPS.Memory_CD8_T_cells_STAT1 LPS.Memory_CD8_T_cells_STAT1
## LPS.Memory_CD8_T_cells_STAT3 LPS.Memory_CD8_T_cells_STAT3
## LPS.Memory_CD8_T_cells_S6 LPS.Memory_CD8_T_cells_S6
## LPS.Memory_CD8_T_cells_MAPKAPK2 LPS.Memory_CD8_T_cells_MAPKAPK2
## LPS.Memory_CD8_T_cells_IkB LPS.Memory_CD8_T_cells_IkB
## LPS.Memory_CD8_T_cells_NFkB LPS.Memory_CD8_T_cells_NFkB
## LPS.Memory_CD8_T_cells_ERK LPS.Memory_CD8_T_cells_ERK
## LPS.B_cells_CREB LPS.B_cells_CREB
## LPS.B_cells_STAT5 LPS.B_cells_STAT5
## LPS.B_cells_p38 LPS.B_cells_p38
## LPS.B_cells_STAT1 LPS.B_cells_STAT1
## LPS.B_cells_STAT3 LPS.B_cells_STAT3
## LPS.B_cells_S6 LPS.B_cells_S6
## LPS.B_cells_MAPKAPK2 LPS.B_cells_MAPKAPK2
## LPS.B_cells_IkB LPS.B_cells_IkB
## LPS.B_cells_NFkB LPS.B_cells_NFkB
## LPS.B_cells_ERK LPS.B_cells_ERK
## LPS.Classical_monocytes_CREB LPS.Classical_monocytes_CREB
## LPS.Classical_monocytes_STAT5 LPS.Classical_monocytes_STAT5
## LPS.Classical_monocytes_p38 LPS.Classical_monocytes_p38
## LPS.Classical_monocytes_STAT1 LPS.Classical_monocytes_STAT1
## LPS.Classical_monocytes_STAT3 LPS.Classical_monocytes_STAT3
## LPS.Classical_monocytes_S6 LPS.Classical_monocytes_S6
## LPS.Classical_monocytes_MAPKAPK2 LPS.Classical_monocytes_MAPKAPK2
## LPS.Classical_monocytes_IkB LPS.Classical_monocytes_IkB
## LPS.Classical_monocytes_NFkB LPS.Classical_monocytes_NFkB
## LPS.Classical_monocytes_ERK LPS.Classical_monocytes_ERK
## LPS.Nonclassical_monocytes_CREB LPS.Nonclassical_monocytes_CREB
## LPS.Nonclassical_monocytes_STAT5 LPS.Nonclassical_monocytes_STAT5
## LPS.Nonclassical_monocytes_p38 LPS.Nonclassical_monocytes_p38
## LPS.Nonclassical_monocytes_STAT1 LPS.Nonclassical_monocytes_STAT1
## LPS.Nonclassical_monocytes_STAT3 LPS.Nonclassical_monocytes_STAT3
## LPS.Nonclassical_monocytes_S6 LPS.Nonclassical_monocytes_S6
## LPS.Nonclassical_monocytes_MAPKAPK2 LPS.Nonclassical_monocytes_MAPKAPK2
## LPS.Nonclassical_monocytes_IkB LPS.Nonclassical_monocytes_IkB
## LPS.Nonclassical_monocytes_NFkB LPS.Nonclassical_monocytes_NFkB
## LPS.Nonclassical_monocytes_ERK LPS.Nonclassical_monocytes_ERK
## LPS.cDCs_CREB LPS.cDCs_CREB
## LPS.cDCs_STAT5 LPS.cDCs_STAT5
## LPS.cDCs_p38 LPS.cDCs_p38
## LPS.cDCs_STAT1 LPS.cDCs_STAT1
## LPS.cDCs_STAT3 LPS.cDCs_STAT3
## LPS.cDCs_S6 LPS.cDCs_S6
## LPS.cDCs_MAPKAPK2 LPS.cDCs_MAPKAPK2
## LPS.cDCs_IkB LPS.cDCs_IkB
## LPS.cDCs_NFkB LPS.cDCs_NFkB
## LPS.cDCs_ERK LPS.cDCs_ERK
## LPS.pDCs_CREB LPS.pDCs_CREB
## LPS.pDCs_STAT5 LPS.pDCs_STAT5
## LPS.pDCs_p38 LPS.pDCs_p38
## LPS.pDCs_STAT1 LPS.pDCs_STAT1
## LPS.pDCs_STAT3 LPS.pDCs_STAT3
## LPS.pDCs_S6 LPS.pDCs_S6
## LPS.pDCs_MAPKAPK2 LPS.pDCs_MAPKAPK2
## LPS.pDCs_IkB LPS.pDCs_IkB
## LPS.pDCs_NFkB LPS.pDCs_NFkB
## LPS.pDCs_ERK LPS.pDCs_ERK
## LPS.Th1_T_cells_CREB LPS.Th1_T_cells_CREB
## LPS.Th1_T_cells_STAT5 LPS.Th1_T_cells_STAT5
## LPS.Th1_T_cells_p38 LPS.Th1_T_cells_p38
## LPS.Th1_T_cells_STAT1 LPS.Th1_T_cells_STAT1
## LPS.Th1_T_cells_STAT3 LPS.Th1_T_cells_STAT3
## LPS.Th1_T_cells_S6 LPS.Th1_T_cells_S6
## LPS.Th1_T_cells_MAPKAPK2 LPS.Th1_T_cells_MAPKAPK2
## LPS.Th1_T_cells_IkB LPS.Th1_T_cells_IkB
## LPS.Th1_T_cells_NFkB LPS.Th1_T_cells_NFkB
## LPS.Th1_T_cells_ERK LPS.Th1_T_cells_ERK
## LPS.Intermediate_monocytes_CREB LPS.Intermediate_monocytes_CREB
## LPS.Intermediate_monocytes_STAT5 LPS.Intermediate_monocytes_STAT5
## LPS.Intermediate_monocytes_p38 LPS.Intermediate_monocytes_p38
## LPS.Intermediate_monocytes_STAT1 LPS.Intermediate_monocytes_STAT1
## LPS.Intermediate_monocytes_STAT3 LPS.Intermediate_monocytes_STAT3
## LPS.Intermediate_monocytes_S6 LPS.Intermediate_monocytes_S6
## LPS.Intermediate_monocytes_MAPKAPK2 LPS.Intermediate_monocytes_MAPKAPK2
## LPS.Intermediate_monocytes_IkB LPS.Intermediate_monocytes_IkB
## LPS.Intermediate_monocytes_NFkB LPS.Intermediate_monocytes_NFkB
## LPS.Intermediate_monocytes_ERK LPS.Intermediate_monocytes_ERK
## LPS.MDSCs_CREB LPS.MDSCs_CREB
## LPS.MDSCs_STAT5 LPS.MDSCs_STAT5
## LPS.MDSCs_p38 LPS.MDSCs_p38
## LPS.MDSCs_STAT1 LPS.MDSCs_STAT1
## LPS.MDSCs_STAT3 LPS.MDSCs_STAT3
## LPS.MDSCs_S6 LPS.MDSCs_S6
## LPS.MDSCs_MAPKAPK2 LPS.MDSCs_MAPKAPK2
## LPS.MDSCs_IkB LPS.MDSCs_IkB
## LPS.MDSCs_NFkB LPS.MDSCs_NFkB
## LPS.MDSCs_ERK LPS.MDSCs_ERK
## LPS.Tregs_CREB LPS.Tregs_CREB
## LPS.Tregs_STAT5 LPS.Tregs_STAT5
## LPS.Tregs_p38 LPS.Tregs_p38
## LPS.Tregs_STAT1 LPS.Tregs_STAT1
## LPS.Tregs_STAT3 LPS.Tregs_STAT3
## LPS.Tregs_S6 LPS.Tregs_S6
## LPS.Tregs_MAPKAPK2 LPS.Tregs_MAPKAPK2
## LPS.Tregs_IkB LPS.Tregs_IkB
## LPS.Tregs_NFkB LPS.Tregs_NFkB
## LPS.Tregs_ERK LPS.Tregs_ERK
## LPS.CD56lo_NK_cells_CREB LPS.CD56lo_NK_cells_CREB
## LPS.CD56lo_NK_cells_STAT5 LPS.CD56lo_NK_cells_STAT5
## LPS.CD56lo_NK_cells_p38 LPS.CD56lo_NK_cells_p38
## LPS.CD56lo_NK_cells_STAT1 LPS.CD56lo_NK_cells_STAT1
## LPS.CD56lo_NK_cells_STAT3 LPS.CD56lo_NK_cells_STAT3
## LPS.CD56lo_NK_cells_S6 LPS.CD56lo_NK_cells_S6
## LPS.CD56lo_NK_cells_MAPKAPK2 LPS.CD56lo_NK_cells_MAPKAPK2
## LPS.CD56lo_NK_cells_IkB LPS.CD56lo_NK_cells_IkB
## LPS.CD56lo_NK_cells_NFkB LPS.CD56lo_NK_cells_NFkB
## LPS.CD56lo_NK_cells_ERK LPS.CD56lo_NK_cells_ERK
## LPS.CD56hi_NK_cells_CREB LPS.CD56hi_NK_cells_CREB
## LPS.CD56hi_NK_cells_STAT5 LPS.CD56hi_NK_cells_STAT5
## LPS.CD56hi_NK_cells_p38 LPS.CD56hi_NK_cells_p38
## LPS.CD56hi_NK_cells_STAT1 LPS.CD56hi_NK_cells_STAT1
## LPS.CD56hi_NK_cells_STAT3 LPS.CD56hi_NK_cells_STAT3
## LPS.CD56hi_NK_cells_S6 LPS.CD56hi_NK_cells_S6
## LPS.CD56hi_NK_cells_MAPKAPK2 LPS.CD56hi_NK_cells_MAPKAPK2
## LPS.CD56hi_NK_cells_IkB LPS.CD56hi_NK_cells_IkB
## LPS.CD56hi_NK_cells_NFkB LPS.CD56hi_NK_cells_NFkB
## LPS.CD56hi_NK_cells_ERK LPS.CD56hi_NK_cells_ERK
## LPS.gd_T_cells_CREB LPS.gd_T_cells_CREB
## LPS.gd_T_cells_STAT5 LPS.gd_T_cells_STAT5
## LPS.gd_T_cells_p38 LPS.gd_T_cells_p38
## LPS.gd_T_cells_STAT1 LPS.gd_T_cells_STAT1
## LPS.gd_T_cells_STAT3 LPS.gd_T_cells_STAT3
## LPS.gd_T_cells_S6 LPS.gd_T_cells_S6
## LPS.gd_T_cells_MAPKAPK2 LPS.gd_T_cells_MAPKAPK2
## LPS.gd_T_cells_IkB LPS.gd_T_cells_IkB
## LPS.gd_T_cells_NFkB LPS.gd_T_cells_NFkB
## LPS.gd_T_cells_ERK LPS.gd_T_cells_ERK
## LPS.Memory_CD4_T_cells_CREB LPS.Memory_CD4_T_cells_CREB
## LPS.Memory_CD4_T_cells_STAT5 LPS.Memory_CD4_T_cells_STAT5
## LPS.Memory_CD4_T_cells_p38 LPS.Memory_CD4_T_cells_p38
## LPS.Memory_CD4_T_cells_STAT1 LPS.Memory_CD4_T_cells_STAT1
## LPS.Memory_CD4_T_cells_STAT3 LPS.Memory_CD4_T_cells_STAT3
## LPS.Memory_CD4_T_cells_S6 LPS.Memory_CD4_T_cells_S6
## LPS.Memory_CD4_T_cells_MAPKAPK2 LPS.Memory_CD4_T_cells_MAPKAPK2
## LPS.Memory_CD4_T_cells_IkB LPS.Memory_CD4_T_cells_IkB
## LPS.Memory_CD4_T_cells_NFkB LPS.Memory_CD4_T_cells_NFkB
## LPS.Memory_CD4_T_cells_ERK LPS.Memory_CD4_T_cells_ERK
## Cocktail.Granulocytes_CREB Cocktail.Granulocytes_CREB
## Cocktail.Granulocytes_STAT5 Cocktail.Granulocytes_STAT5
## Cocktail.Granulocytes_p38 Cocktail.Granulocytes_p38
## Cocktail.Granulocytes_STAT1 Cocktail.Granulocytes_STAT1
## Cocktail.Granulocytes_STAT3 Cocktail.Granulocytes_STAT3
## Cocktail.Granulocytes_S6 Cocktail.Granulocytes_S6
## Cocktail.Granulocytes_MAPKAPK2 Cocktail.Granulocytes_MAPKAPK2
## Cocktail.Granulocytes_IkB Cocktail.Granulocytes_IkB
## Cocktail.Granulocytes_NFkB Cocktail.Granulocytes_NFkB
## Cocktail.Granulocytes_ERK Cocktail.Granulocytes_ERK
## Cocktail.CD8_T_cells_CREB Cocktail.CD8_T_cells_CREB
## Cocktail.CD8_T_cells_STAT5 Cocktail.CD8_T_cells_STAT5
## Cocktail.CD8_T_cells_p38 Cocktail.CD8_T_cells_p38
## Cocktail.CD8_T_cells_STAT1 Cocktail.CD8_T_cells_STAT1
## Cocktail.CD8_T_cells_STAT3 Cocktail.CD8_T_cells_STAT3
## Cocktail.CD8_T_cells_S6 Cocktail.CD8_T_cells_S6
## Cocktail.CD8_T_cells_MAPKAPK2 Cocktail.CD8_T_cells_MAPKAPK2
## Cocktail.CD8_T_cells_IkB Cocktail.CD8_T_cells_IkB
## Cocktail.CD8_T_cells_NFkB Cocktail.CD8_T_cells_NFkB
## Cocktail.CD8_T_cells_ERK Cocktail.CD8_T_cells_ERK
## Cocktail.CD4_T_cells_CREB Cocktail.CD4_T_cells_CREB
## Cocktail.CD4_T_cells_STAT5 Cocktail.CD4_T_cells_STAT5
## Cocktail.CD4_T_cells_p38 Cocktail.CD4_T_cells_p38
## Cocktail.CD4_T_cells_STAT1 Cocktail.CD4_T_cells_STAT1
## Cocktail.CD4_T_cells_STAT3 Cocktail.CD4_T_cells_STAT3
## Cocktail.CD4_T_cells_S6 Cocktail.CD4_T_cells_S6
## Cocktail.CD4_T_cells_MAPKAPK2 Cocktail.CD4_T_cells_MAPKAPK2
## Cocktail.CD4_T_cells_IkB Cocktail.CD4_T_cells_IkB
## Cocktail.CD4_T_cells_NFkB Cocktail.CD4_T_cells_NFkB
## Cocktail.CD4_T_cells_ERK Cocktail.CD4_T_cells_ERK
## Cocktail.Naive_CD4_T_cells_CREB Cocktail.Naive_CD4_T_cells_CREB
## Cocktail.Naive_CD4_T_cells_STAT5 Cocktail.Naive_CD4_T_cells_STAT5
## Cocktail.Naive_CD4_T_cells_p38 Cocktail.Naive_CD4_T_cells_p38
## Cocktail.Naive_CD4_T_cells_STAT1 Cocktail.Naive_CD4_T_cells_STAT1
## Cocktail.Naive_CD4_T_cells_STAT3 Cocktail.Naive_CD4_T_cells_STAT3
## Cocktail.Naive_CD4_T_cells_S6 Cocktail.Naive_CD4_T_cells_S6
## Cocktail.Naive_CD4_T_cells_MAPKAPK2 Cocktail.Naive_CD4_T_cells_MAPKAPK2
## Cocktail.Naive_CD4_T_cells_IkB Cocktail.Naive_CD4_T_cells_IkB
## Cocktail.Naive_CD4_T_cells_NFkB Cocktail.Naive_CD4_T_cells_NFkB
## Cocktail.Naive_CD4_T_cells_ERK Cocktail.Naive_CD4_T_cells_ERK
## Cocktail.Naive_CD8_T_cells_CREB Cocktail.Naive_CD8_T_cells_CREB
## Cocktail.Naive_CD8_T_cells_STAT5 Cocktail.Naive_CD8_T_cells_STAT5
## Cocktail.Naive_CD8_T_cells_p38 Cocktail.Naive_CD8_T_cells_p38
## Cocktail.Naive_CD8_T_cells_STAT1 Cocktail.Naive_CD8_T_cells_STAT1
## Cocktail.Naive_CD8_T_cells_STAT3 Cocktail.Naive_CD8_T_cells_STAT3
## Cocktail.Naive_CD8_T_cells_S6 Cocktail.Naive_CD8_T_cells_S6
## Cocktail.Naive_CD8_T_cells_MAPKAPK2 Cocktail.Naive_CD8_T_cells_MAPKAPK2
## Cocktail.Naive_CD8_T_cells_IkB Cocktail.Naive_CD8_T_cells_IkB
## Cocktail.Naive_CD8_T_cells_NFkB Cocktail.Naive_CD8_T_cells_NFkB
## Cocktail.Naive_CD8_T_cells_ERK Cocktail.Naive_CD8_T_cells_ERK
## Cocktail.Memory_CD8_T_cells_CREB Cocktail.Memory_CD8_T_cells_CREB
## Cocktail.Memory_CD8_T_cells_STAT5 Cocktail.Memory_CD8_T_cells_STAT5
## Cocktail.Memory_CD8_T_cells_p38 Cocktail.Memory_CD8_T_cells_p38
## Cocktail.Memory_CD8_T_cells_STAT1 Cocktail.Memory_CD8_T_cells_STAT1
## Cocktail.Memory_CD8_T_cells_STAT3 Cocktail.Memory_CD8_T_cells_STAT3
## Cocktail.Memory_CD8_T_cells_S6 Cocktail.Memory_CD8_T_cells_S6
## Cocktail.Memory_CD8_T_cells_MAPKAPK2 Cocktail.Memory_CD8_T_cells_MAPKAPK2
## Cocktail.Memory_CD8_T_cells_IkB Cocktail.Memory_CD8_T_cells_IkB
## Cocktail.Memory_CD8_T_cells_NFkB Cocktail.Memory_CD8_T_cells_NFkB
## Cocktail.Memory_CD8_T_cells_ERK Cocktail.Memory_CD8_T_cells_ERK
## Cocktail.B_cells_CREB Cocktail.B_cells_CREB
## Cocktail.B_cells_STAT5 Cocktail.B_cells_STAT5
## Cocktail.B_cells_p38 Cocktail.B_cells_p38
## Cocktail.B_cells_STAT1 Cocktail.B_cells_STAT1
## Cocktail.B_cells_STAT3 Cocktail.B_cells_STAT3
## Cocktail.B_cells_S6 Cocktail.B_cells_S6
## Cocktail.B_cells_MAPKAPK2 Cocktail.B_cells_MAPKAPK2
## Cocktail.B_cells_IkB Cocktail.B_cells_IkB
## Cocktail.B_cells_NFkB Cocktail.B_cells_NFkB
## Cocktail.B_cells_ERK Cocktail.B_cells_ERK
## Cocktail.Classical_monocytes_CREB Cocktail.Classical_monocytes_CREB
## Cocktail.Classical_monocytes_STAT5 Cocktail.Classical_monocytes_STAT5
## Cocktail.Classical_monocytes_p38 Cocktail.Classical_monocytes_p38
## Cocktail.Classical_monocytes_STAT1 Cocktail.Classical_monocytes_STAT1
## Cocktail.Classical_monocytes_STAT3 Cocktail.Classical_monocytes_STAT3
## Cocktail.Classical_monocytes_S6 Cocktail.Classical_monocytes_S6
## Cocktail.Classical_monocytes_MAPKAPK2 Cocktail.Classical_monocytes_MAPKAPK2
## Cocktail.Classical_monocytes_IkB Cocktail.Classical_monocytes_IkB
## Cocktail.Classical_monocytes_NFkB Cocktail.Classical_monocytes_NFkB
## Cocktail.Classical_monocytes_ERK Cocktail.Classical_monocytes_ERK
## Cocktail.Nonclassical_monocytes_CREB Cocktail.Nonclassical_monocytes_CREB
## Cocktail.Nonclassical_monocytes_STAT5 Cocktail.Nonclassical_monocytes_STAT5
## Cocktail.Nonclassical_monocytes_p38 Cocktail.Nonclassical_monocytes_p38
## Cocktail.Nonclassical_monocytes_STAT1 Cocktail.Nonclassical_monocytes_STAT1
## Cocktail.Nonclassical_monocytes_STAT3 Cocktail.Nonclassical_monocytes_STAT3
## Cocktail.Nonclassical_monocytes_S6 Cocktail.Nonclassical_monocytes_S6
## Cocktail.Nonclassical_monocytes_MAPKAPK2 Cocktail.Nonclassical_monocytes_MAPKAPK2
## Cocktail.Nonclassical_monocytes_IkB Cocktail.Nonclassical_monocytes_IkB
## Cocktail.Nonclassical_monocytes_NFkB Cocktail.Nonclassical_monocytes_NFkB
## Cocktail.Nonclassical_monocytes_ERK Cocktail.Nonclassical_monocytes_ERK
## Cocktail.cDCs_CREB Cocktail.cDCs_CREB
## Cocktail.cDCs_STAT5 Cocktail.cDCs_STAT5
## Cocktail.cDCs_p38 Cocktail.cDCs_p38
## Cocktail.cDCs_STAT1 Cocktail.cDCs_STAT1
## Cocktail.cDCs_STAT3 Cocktail.cDCs_STAT3
## Cocktail.cDCs_S6 Cocktail.cDCs_S6
## Cocktail.cDCs_MAPKAPK2 Cocktail.cDCs_MAPKAPK2
## Cocktail.cDCs_IkB Cocktail.cDCs_IkB
## Cocktail.cDCs_NFkB Cocktail.cDCs_NFkB
## Cocktail.cDCs_ERK Cocktail.cDCs_ERK
## Cocktail.pDCs_CREB Cocktail.pDCs_CREB
## Cocktail.pDCs_STAT5 Cocktail.pDCs_STAT5
## Cocktail.pDCs_p38 Cocktail.pDCs_p38
## Cocktail.pDCs_STAT1 Cocktail.pDCs_STAT1
## Cocktail.pDCs_STAT3 Cocktail.pDCs_STAT3
## Cocktail.pDCs_S6 Cocktail.pDCs_S6
## Cocktail.pDCs_MAPKAPK2 Cocktail.pDCs_MAPKAPK2
## Cocktail.pDCs_IkB Cocktail.pDCs_IkB
## Cocktail.pDCs_NFkB Cocktail.pDCs_NFkB
## Cocktail.pDCs_ERK Cocktail.pDCs_ERK
## Cocktail.Th1_T_cells_CREB Cocktail.Th1_T_cells_CREB
## Cocktail.Th1_T_cells_STAT5 Cocktail.Th1_T_cells_STAT5
## Cocktail.Th1_T_cells_p38 Cocktail.Th1_T_cells_p38
## Cocktail.Th1_T_cells_STAT1 Cocktail.Th1_T_cells_STAT1
## Cocktail.Th1_T_cells_STAT3 Cocktail.Th1_T_cells_STAT3
## Cocktail.Th1_T_cells_S6 Cocktail.Th1_T_cells_S6
## Cocktail.Th1_T_cells_MAPKAPK2 Cocktail.Th1_T_cells_MAPKAPK2
## Cocktail.Th1_T_cells_IkB Cocktail.Th1_T_cells_IkB
## Cocktail.Th1_T_cells_NFkB Cocktail.Th1_T_cells_NFkB
## Cocktail.Th1_T_cells_ERK Cocktail.Th1_T_cells_ERK
## Cocktail.Intermediate_monocytes_CREB Cocktail.Intermediate_monocytes_CREB
## Cocktail.Intermediate_monocytes_STAT5 Cocktail.Intermediate_monocytes_STAT5
## Cocktail.Intermediate_monocytes_p38 Cocktail.Intermediate_monocytes_p38
## Cocktail.Intermediate_monocytes_STAT1 Cocktail.Intermediate_monocytes_STAT1
## Cocktail.Intermediate_monocytes_STAT3 Cocktail.Intermediate_monocytes_STAT3
## Cocktail.Intermediate_monocytes_S6 Cocktail.Intermediate_monocytes_S6
## Cocktail.Intermediate_monocytes_MAPKAPK2 Cocktail.Intermediate_monocytes_MAPKAPK2
## Cocktail.Intermediate_monocytes_IkB Cocktail.Intermediate_monocytes_IkB
## Cocktail.Intermediate_monocytes_NFkB Cocktail.Intermediate_monocytes_NFkB
## Cocktail.Intermediate_monocytes_ERK Cocktail.Intermediate_monocytes_ERK
## Cocktail.MDSCs_CREB Cocktail.MDSCs_CREB
## Cocktail.MDSCs_STAT5 Cocktail.MDSCs_STAT5
## Cocktail.MDSCs_p38 Cocktail.MDSCs_p38
## Cocktail.MDSCs_STAT1 Cocktail.MDSCs_STAT1
## Cocktail.MDSCs_STAT3 Cocktail.MDSCs_STAT3
## Cocktail.MDSCs_S6 Cocktail.MDSCs_S6
## Cocktail.MDSCs_MAPKAPK2 Cocktail.MDSCs_MAPKAPK2
## Cocktail.MDSCs_IkB Cocktail.MDSCs_IkB
## Cocktail.MDSCs_NFkB Cocktail.MDSCs_NFkB
## Cocktail.MDSCs_ERK Cocktail.MDSCs_ERK
## Cocktail.Tregs_CREB Cocktail.Tregs_CREB
## Cocktail.Tregs_STAT5 Cocktail.Tregs_STAT5
## Cocktail.Tregs_p38 Cocktail.Tregs_p38
## Cocktail.Tregs_STAT1 Cocktail.Tregs_STAT1
## Cocktail.Tregs_STAT3 Cocktail.Tregs_STAT3
## Cocktail.Tregs_S6 Cocktail.Tregs_S6
## Cocktail.Tregs_MAPKAPK2 Cocktail.Tregs_MAPKAPK2
## Cocktail.Tregs_IkB Cocktail.Tregs_IkB
## Cocktail.Tregs_NFkB Cocktail.Tregs_NFkB
## Cocktail.Tregs_ERK Cocktail.Tregs_ERK
## Cocktail.CD56lo_NK_cells_CREB Cocktail.CD56lo_NK_cells_CREB
## Cocktail.CD56lo_NK_cells_STAT5 Cocktail.CD56lo_NK_cells_STAT5
## Cocktail.CD56lo_NK_cells_p38 Cocktail.CD56lo_NK_cells_p38
## Cocktail.CD56lo_NK_cells_STAT1 Cocktail.CD56lo_NK_cells_STAT1
## Cocktail.CD56lo_NK_cells_STAT3 Cocktail.CD56lo_NK_cells_STAT3
## Cocktail.CD56lo_NK_cells_S6 Cocktail.CD56lo_NK_cells_S6
## Cocktail.CD56lo_NK_cells_MAPKAPK2 Cocktail.CD56lo_NK_cells_MAPKAPK2
## Cocktail.CD56lo_NK_cells_IkB Cocktail.CD56lo_NK_cells_IkB
## Cocktail.CD56lo_NK_cells_NFkB Cocktail.CD56lo_NK_cells_NFkB
## Cocktail.CD56lo_NK_cells_ERK Cocktail.CD56lo_NK_cells_ERK
## Cocktail.CD56hi_NK_cells_CREB Cocktail.CD56hi_NK_cells_CREB
## Cocktail.CD56hi_NK_cells_STAT5 Cocktail.CD56hi_NK_cells_STAT5
## Cocktail.CD56hi_NK_cells_p38 Cocktail.CD56hi_NK_cells_p38
## Cocktail.CD56hi_NK_cells_STAT1 Cocktail.CD56hi_NK_cells_STAT1
## Cocktail.CD56hi_NK_cells_STAT3 Cocktail.CD56hi_NK_cells_STAT3
## Cocktail.CD56hi_NK_cells_S6 Cocktail.CD56hi_NK_cells_S6
## Cocktail.CD56hi_NK_cells_MAPKAPK2 Cocktail.CD56hi_NK_cells_MAPKAPK2
## Cocktail.CD56hi_NK_cells_IkB Cocktail.CD56hi_NK_cells_IkB
## Cocktail.CD56hi_NK_cells_NFkB Cocktail.CD56hi_NK_cells_NFkB
## Cocktail.CD56hi_NK_cells_ERK Cocktail.CD56hi_NK_cells_ERK
## Cocktail.gd_T_cells_CREB Cocktail.gd_T_cells_CREB
## Cocktail.gd_T_cells_STAT5 Cocktail.gd_T_cells_STAT5
## Cocktail.gd_T_cells_p38 Cocktail.gd_T_cells_p38
## Cocktail.gd_T_cells_STAT1 Cocktail.gd_T_cells_STAT1
## Cocktail.gd_T_cells_STAT3 Cocktail.gd_T_cells_STAT3
## Cocktail.gd_T_cells_S6 Cocktail.gd_T_cells_S6
## Cocktail.gd_T_cells_MAPKAPK2 Cocktail.gd_T_cells_MAPKAPK2
## Cocktail.gd_T_cells_IkB Cocktail.gd_T_cells_IkB
## Cocktail.gd_T_cells_NFkB Cocktail.gd_T_cells_NFkB
## Cocktail.gd_T_cells_ERK Cocktail.gd_T_cells_ERK
## Cocktail.Memory_CD4_T_cells_CREB Cocktail.Memory_CD4_T_cells_CREB
## Cocktail.Memory_CD4_T_cells_STAT5 Cocktail.Memory_CD4_T_cells_STAT5
## Cocktail.Memory_CD4_T_cells_p38 Cocktail.Memory_CD4_T_cells_p38
## Cocktail.Memory_CD4_T_cells_STAT1 Cocktail.Memory_CD4_T_cells_STAT1
## Cocktail.Memory_CD4_T_cells_STAT3 Cocktail.Memory_CD4_T_cells_STAT3
## Cocktail.Memory_CD4_T_cells_S6 Cocktail.Memory_CD4_T_cells_S6
## Cocktail.Memory_CD4_T_cells_MAPKAPK2 Cocktail.Memory_CD4_T_cells_MAPKAPK2
## Cocktail.Memory_CD4_T_cells_IkB Cocktail.Memory_CD4_T_cells_IkB
## Cocktail.Memory_CD4_T_cells_NFkB Cocktail.Memory_CD4_T_cells_NFkB
## Cocktail.Memory_CD4_T_cells_ERK Cocktail.Memory_CD4_T_cells_ERK
For abundance:
# for abundance version
mom_df <- percents_df %>% dplyr::filter(SampleType == "M") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
baby_df <- percents_df %>% dplyr::filter(SampleType == "B") %>% dplyr::select(-filename, -Pair, -SampleType, -Condition, -Individual)
paired_pvals <- mapply(function(x, y) t.test(x,y, paired = TRUE)$p.value, mom_df, baby_df)
unpaired_pvals <- mapply(function(x, y) t.test(x,y, paired = FALSE)$p.value, mom_df, baby_df)
# plot(-log(unpaired_pvals), -log(paired_pvals))
# Number of comparisons: 20 cell types x 10 phosphos x 3 conditions
bonf <- .05/(ncol(mom_df))
significance <- vector(mode = "character", length = length(unpaired_pvals))
significance[(unpaired_pvals < bonf) & (paired_pvals < bonf)] <- "Both"
significance[(unpaired_pvals < bonf) & (paired_pvals > bonf)] <- "Unpaired only"
significance[(unpaired_pvals > bonf) & (paired_pvals < bonf)] <- "Paired only"
significance[(unpaired_pvals > bonf) & (paired_pvals > bonf)] <- "Not significant"
plot_df <- data.frame(unpaired_pvals, paired_pvals, Significance = significance, Features = names(paired_pvals))
p <- ggplot(plot_df, aes(-log(unpaired_pvals), -log(paired_pvals))) +
geom_point(size = 1, aes(colour = Significance)) +
scale_color_manual(values=c("blue", " dark gray", "red", "orange"))
print(p)
plot_df %>% dplyr::filter(Significance != "Not significant") %>%
dplyr::select(-unpaired_pvals) %>%
dplyr::select(-paired_pvals)
## Significance Features
## 1 Both CD8_T_cells_Percent_Total
## 2 Paired only Memory_CD8_T_cells_Percent_Total
## 3 Both B_cells_Percent_Total
## 4 Unpaired only pDCs_Percent_Total
## 5 Both Memory_CD4_T_cells_Percent_Total
## 6 Unpaired only Granulocytes_Percent_Total